Clinical phenotypes and cochlear implant outcomes in patients with PTPN11-associated noonan spectrum disorders: Insights from a genetically screened cohort

Abstract

Objectives

We characterized the clinical features of PTPN11-related deafness and evaluated the outcomes of cochlear implantation in affected patients.

Methods

Whole-exome sequencing and bioinformatic analyses were performed in a cohort of 467 individuals with congenital sensorineural hearing loss to identify potential genetic etiologies. Four patients harboring PTPN11 variants were reviewed for their clinical characteristics and post-implantation auditory rehabilitation outcomes.

Results

PTPN11 variants were identified in four patients (Cases 1–4). A missense variant c.1391G > C (p.Gly464Ala) in exon 12 was detected in Case 1 and the recurrent variant c.836A > G (p.Tyr279Cys) in exon 7 was identified in Case 2. Both patients were diagnosed with Noonan syndrome with multiple lentigines. Missense variants c.1510A > G (p.Met504Val) in exon 13 and c.923A > G (p.Asn308Ser) in exon 8 were found in Cases 3 and 4, respectively; both were diagnosed with Noonan syndrome. Cases 1, 2, and 4 underwent cochlear implantation and demonstrated favorable postoperative auditory and speech outcomes.

Conclusion

Our study provides a comprehensive characterization of auditory, speech and systemic phenotypes in PTPN11-related Noonan spectrum disorders and demonstrates that cochlear implantation is highly effective for severe-to-profound hearing loss. These findings emphasize the value of early genetic diagnosis and emphasize the importance of coordinated, interdisciplinary management.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00405-026-10056-8.

Introduction

Genetic deafness can be categorized into syndromic and non-syndromic forms. To date, more than 400 syndromic types of deafness have been identified, in which hearing loss is accompanied by a range of other systemic abnormalities. Syndromic forms account for approximately 30% of hereditary hearing loss [1]. These conditions not only result in auditory impairment but also are frequently associated with multisystem involvement, including cardiac, renal, and visual abnormalities that substantially affect patients’ quality of life. In clinical practice, diagnosis and management of syndromic hearing loss remain particularly challenging due to their marked genetic and phenotypic heterogeneity [2]. In our previous studies, we characterized the broad genetic heterogeneity of congenital hearing impairment and identified novel candidate genes associated with this condition [3, 4]. To achieve this, whole-exome sequencing (WES) combined with bioinformatic trio analysis was performed on probands and their parents. Through this approach, four patients were found to harbor pathogenic variants in PTPN11. The human PTPN11 gene (OMIM 600568), located on chromosome 12q24, encodes the ubiquitously expressed non-receptor protein tyrosine phosphatase Src-Homology domain-2 containing protein tyrosine Phosphatase 2 (SHP-2), a critical member of the protein tyrosine phosphatase (PTP) superfamily. SHP-2 regulates essential cellular processes, including cell proliferation, differentiation, cell cycle progression, and oncogenic transformation, primarily through its catalytic activity [5]. Under physiological conditions, SHP-2 functions as a key regulator of multiple signaling pathways involved in cell proliferation and survival. The genetic disorders collectively known as RASopathies involve dysregulation of the RAS–mitogen-activated protein kinase (RAS/MAPK) and phosphoinositide 3-kinase (PI3K)/AKT signaling cascades. Germline variants in the PTPN11 gene cause Noonan syndrome (NS; MIM #163,950) and Noonan syndrome with multiple lentigines (NS-ML; MIM #151,100), formerly referred to as LEOPARD syndrome. The latter is a rare multisystemic disorder that shares several clinical features with NS and is characterized by multiple lentigines, electrocardiographic conduction abnormalities, ocular hypertelorism, pulmonary stenosis, abnormal genitalia, growth retardation, and SNHL [6]. To date, approximately one-fourth of individuals with PTPN11 variants exhibit hearing loss. Wu et al. [7] reported that among 85 patients with PTPN11-related NS, hearing loss was predominantly moderate to severe and was frequently associated with structural abnormalities of the inner ear and auditory nerve (48/85). Similarly, Gao et al. [8] suggested that congenital sensorineural hearing loss (SNHL) may represent an early manifestation of PTPN11-related NS. However, the prevalence and mechanisms of SNHL in RASopathy-associated NS remain uncertain [9]. Moreover, few studies have investigated PTPN11 variant-induced SNHL or the corresponding auditory rehabilitation outcomes, limiting insights into the genotype–phenotype correlations underlying NS and NS-ML [9]. We characterized the clinical and audiological features of PTPN11-related deafness, ascertained the phenotypic spectrum of associated polymalformative syndromes, and evaluated cochlear implant performance in affected patients. These findings may provide valuable evidence to guide clinical diagnosis and management.

Materials and methods

Patients

Our study was conducted as a retrospective case series within a genetically screened cohort. In total, 467 individuals affected by syndromic or non-syndromic hearing loss were subjected to WES. The Ethics Committee of the China-Japan Friendship Hospital approved the study protocol (approval No. 2023-KY-217–1). Written informed consent was obtained from all adult participants, and from the parents or legal guardians of minors under 18 years of age, prior to enrollment.

Trio WES and pathogenic variant analysis of the PTPN11

Whole-blood samples (5 mL per participant) were collected via standard venipuncture from probands and their phenotypically normal parents, forming matched trio sample sets for downstream analysis. Genomic DNA was extracted using a Blood Genomic DNA Extraction Kit (Solarbio, Beijing, China) and quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). Exome-enriched libraries were prepared using an Agilent SureSelect Human All Exon V6 kit and sequenced on an Illumina NovaSeq 6000 platform in 150-bp paired-end mode, achieving an average coverage depth of 100 ×. Sequenced reads were aligned to the human reference genome (hg19) using the Burrows–Wheeler Aligner, and variant calling was performed with the Genome Analysis Toolkit (GATK v4.3.0) following the GATK Best Practices workflow, including base quality score recalibration and joint genotyping across all samples. Functional annotation of variants was conducted using ANNOVAR (version 2023.06) with integrated databases, including population frequency (gnomAD v3.1.2), pathogenicity prediction (REVEL, CADD v1.6), and clinical interpretation (ClinVar 2024.01). Variant filtering followed the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG-AMP) guidelines, requiring concordant deleterious predictions from at least three in silico tools and a minor allele frequency < 0.1% in population databases. Selected variants were further validated by confirmatory Sanger sequencing using gene-specific primers.

A schematic diagram of the PTPN11 gene structure was generated using the Biorender online platform (https://www.biorender.com/). The three-dimensional structure of the human PTPN11 protein was obtained from the AlphaFold Protein Structure Database (https://alphafold.ebi.ac.uk) and visualized using PyMOL software (Schrödinger, LLC, New York, NY, USA).

Clinical assessment

For individuals harboring PTPN11 variants, medical history, physical examination, auditory evaluation, electrocardiography, cardiac color Doppler ultrasound, high-resolution temporal bone computed tomography and magnetic resonance imaging were performed (Fig. 1). Comprehensive assessments at the time of clinical diagnosis included audiological and neurodevelopmental evaluations: behavioral audiometry, acoustic immittance, auditory steady-state response (for children < 6 years), distortion product otoacoustic emission, auditory brainstem response and the Griffiths Mental Development Scales for children < 6 years (Table 1). Normal neurodevelopment was defined as a developmental quotient ≥ 85.

Fig. 1.

Multisystem features of two NS-ML cases and one NS case (A) Left-sided ptosis in the female patient (Case 1). She was born with partial duplication of the thumb (preaxial polydactyly), which was surgically corrected; (B) the postoperative scar is shown (white solid line). (C) Echocardiography revealed congenital heart disease with multiple atrial septal defects and left-to-right shunting at the atrial level. (E–I, K) Male patient (Case 2) with NS-ML. Numerous lentigines were distributed predominantly over the upper trunk and face (E–G). Additional findings included ocular hypertelorism (F), a high-arched palate (K) and dental malalignment. A pectus carinatum is visible on the patient’s right side, marked with a white circle (H). (J, L–N) The male patient (Case 4) with a triangular facial contour, low-set, posteriorly rotated ears (J) and dental malalignment (L). Echocardiography demonstrated trace left-to-right shunting at the atrial level, suggestive of a patent foramen ovale, indicated by the green dot in the magnified image (M). NS, Noonan syndrome; NS-ML, Noonan syndrome with multiple lentigines

Table 1.

Preoperative cochlear implant evaluation of four patients with PTPN11 variants

Case No	Case1 NS-ML	Case2 NS-ML	Case 3 NS	Case 4 NS
Age at Diagnosis	1.2 Y/1 Y 6 mo	4 mo/1 Y 11 mo	2 Y/HA	6 mo/1 Y 4 mo
PTA:125–250-0.5.5 K-1 K-2 K-4 K-8 K (Hz/dBHL)	R: 90–90-90–100-100–110-110 L:90–95–100–100-100–100-100	R: 90–90-90–100-100–110-110 L: 90–95–100–100-100–100-100	R: 80–80-75–75–90–85–90 L: 80–80–85–90–95–95-95	R: 95–95–100–100-90–90–95 L: 95–100-100–100-100–100-100
Acoustic immittance	A	A	A	A
ASSR (dBnHL)	Right: 100–105–110–115 Left: 100–105-105–110	Right: 99–114-102–106 Left: 89–104–112–106	Right: 80–80–85–95 Left: 90–100–105–100	Right: 100–105-95–90 Left: 105–100–105–100
DPOAE	No response	No response	No response	No response
ABR threshold (dBnHL)	> 100 dBnHL (bilateral)	> 100 dBnHL (bilateral)	R: 80/L: 90 dBnHL	97 dBnHL (bilateral)
Temporal bone HRCT	Normal	Normal	Normal	Normal
Brain MRI	Normal	Normal	Normal	Normal
GMDS DQ (scores)	97	101	90	95

NS, Noonan syndrome; NS-ML, Noonan syndrome with multiple lentigines; CI, cochlear implantation; PTA, pure-tone audiometry; R, right ear; L, left ear; Y, years; mo, months; Hz, hertz; dB HL, decibels hearing level; dBnHL, decibels normalized hearing level; A, normal acoustic immittance; ASSR, auditory steady-state response; DPOAE, distortion-product otoacoustic emission; ABR, auditory brainstem response; HRCT, high-resolution computed tomography; MRI, magnetic resonance imaging; GMDS, Griffiths Mental Development Scales; DQ, developmental quotient; HA, hearing aid.

CI was performed successfully in three PTPN11-affected patients (Cases 1, 2, and 4) by the same experienced senior surgeon using a posterior tympanotomy approach.

During follow-up, speech perception performance was evaluated using the Speech and Language Rehabilitation Wordlist for Hearing-Impaired Children, developed by Sun et al. [10] The materials were presented in quiet conditions at 65 dBA through a single loudspeaker, with participants seated 1 m directly in front of the sound source. Auditory and speech outcomes were assessed using monosyllabic and bisyllabic word recognition tests, short sentence recognition, the Categories of Auditory Performance (CAP) scale, and the Speech Intelligibility Rating (SIR) scale.

Given the etiological complexity of pediatric hearing loss, a multidisciplinary team (MDT) was established at our institution. The MDT comprised otolaryngologists, audiologists, speech–language pathologists, and specialists in pediatrics, ultrasonography, laboratory medicine, orthopedics, neurology, cardiology, and anesthesiology. [11]

Electrophysiological assessments

Electrically evoked auditory brainstem responses (EABRs) were used to evaluate brainstem auditory pathway function in PTPN11-related CI recipients. Recordings were obtained using Neuro-Audio NET 1.0.103.3 (Neurosoft, Ivanovo, Russia). Positive, negative, and ground electrodes were body-surface button electrodes (impedances < 1 KΩ) positioned on the forehead (at the hairline), contralateral shoulder, and midline between the eyebrows, respectively. Recording parameters included a bandwidth of 100–3 kHz, averaging 500 sweeps per stimulus level, a 15-ms time window, and a ± 10 μV rejection threshold. Testing was conducted after natural sleep; if this was not feasible, chloral hydrate (30–80 mg/kg) was administered to obtain stable and clear EABR waveforms. Stimulus consisted of alternating biphasic pulses in monopolar mode (MP1 + 2) with a pulse width of 37 or 50 μs and an interphase gap of 5 μs. Analyzed EABR measures included wave V input/output function, thresholds, and Gibson scoring, defined and calculated according to previously published methods. [12]

Results

Pathogenic variant analysis of the PTPN11 gene

All PTPN11 variants identified in this cohort were heterozygous missense variants that had been previously reported. The affected residues were highly conserved across orthologous proteins in multiple species. According to the ACMG/AMP guidelines, all variants were classified as pathogenic or likely pathogenic. Table 2 presents the clinical phenotypes and postoperative auditory and speech outcomes of the four cases. No family history suggestive of LEOPARD syndrome or other inherited phenotypes was identified. The Pedigrees of the four families affected by PTPN11 are shown in Fig. 2a. Specifically, a missense variant c.1391G > C (p.Gly464Ala) in exon 12 was detected in Case 1, the recurrent variant c.836A > G (p.Tyr279Cys) in exon 7 was identified in Case 2, a missense variant c.1510A > G (p.Met504Val) in exon 13 was identified in Case 3, and another missense variant c.923A > G (p.Asn308Ser) in exon 8 was detected in Case 4 (Fig. 2b).

Table 2.

Clinical features and CI outcomes of patients with PTPN11 variants

Family ID	Case 1 NS-ML	Case 2 NS-ML	Case 3 NS	Case 4 NS
Age at assessment (Y)	8	8	17	4
Sex	Female	Male	Female	Male
Physical appearance
Poor linear growth/Short stature (centiles)	< 10th	< 25th	< 3rd	< 3rd
Triangular contour of the face	-	-	-	+
Hypertelorism (mm)	36	38	38	34
Ptosis	+	-	-	-
Epicanthus medialis	-	-	-	-
Intellectual disability	-	-	-	-
Cardiovascular malformations
Atrial septal defect	+	-	-	-
Patent foramen ovale	-	-	-	+
ECG abnormality	-	-	-	-
Hypertrophic cardiomyopathy	-	-	-	-
ENT features
Sensorineural hearing loss	Severe to profound	Severe to profound	Severe	Severe to profound
Low-set, posteriorly rotated ears	+	+	+	+
Anatomic middle/inner ear abnormalities	-	-	-	-
High-arched palate	+	+	-	-
Malalignment of teeth	+	+	+	+
Other clinical features
Single transverse palmar crease	-	+	-	-
Splenomegaly	-	+	-	-
Cryptorchidism/undescended testes	-	+	-	-
Abnormal pigmentation/lentigines	+	+	-	-
Cafe-au-lait spots	-	+	-	-
Cystic lymphangioma	-	+	-	-
Pectus carinatum	+	-	-	+
Rib flaring	-	-	-	+
Cubitus valgus	+	-	-	-
Amblyopia	+	-	-	-
Preaxial polydactyly	+	-	-	-
Speech and auditory performance post-CI
Age at CI surgery	1 Y 6 m	1 Y 11 m	Not implanted	1 Y 4 m
CI/processor	R: Hearing Aid L: Nurotron CS-20A (TM)	Bilateral: Cochlea CI 512/CP910	Bilateral: HAs: Oticon Intent 1 mini RITE	L: Cochlea CI 512/N6 R: Hearing Aid
CAP/SIR	9/5	9/5	5/3	8/5
Aided CI Hearing threshold (dB HL, 250Hz–6kHz)	L: 35–40-35–20–25–20 R: 35–55–60–50-50–50	L: 30–40-30–25–30 R: 25–35-30–25-20	NA	L: 35–40-35–40-35 R: 60–70-70–80-80
Monosyllable recognition (closed-set, vowel/consonant, %)	96/96	100/96	NA	96/88
Disyllable Word recognition (closed-set, %)	100	96	NA	100
Short sentence recognition (open-set, %)	100	100	NA	95
Follow-up duration	2 Y	5 Y	4 Y	3 Y

Wide clinical variability of symptoms. Symbols are indicating presence (+) and absence (-) of symptoms; NA, non-available

CI, cochlear implantation; CAP, Categories of Auditory Performance; SIR, Speech Intelligibility Rating; dB HL, decibels hearing level; Y, years; m, months; R, right ear; L, left ear; NA, not available; HAs, hearing aids

Fig. 2.

Distribution of PTPN11 variant sites among the four probands. a Pedigrees of the families with PTPN11 variants; b Structure of the human PTPN11 gene, which comprises 16 exons and encodes a ubiquitously expressed 7-kb transcript containing a 1,779-bp open reading frame. This sequence translates into a 593-amino acid protein consisting of three functional domains: N-SH2 (3–104), C-SH2 (112–216), and PTP (221–524). The amino acid boundaries of the functional domains are indicated. bp, base pair; kb, kilobase; N-SH2, N-terminal Src homology 2; C-SH2, C-terminal Src homology 2; PTP, protein tyrosine phosphatase

Case 1

The proband was an 8-year-old girl with bilateral SNHL and a healthy older brother. Physical examination revealed a grade 3/6 systolic ejection murmur on cardiac auscultation, hypertelorism, low-set posteriorly rotated ears, dental malalignment, a high-arched palate, mild pectus carinatum, widened intermammary distance, malocclusion, cubitus valgus, and amblyopia. No epicanthal folds or neck webbing were present. Left-sided ptosis and growth retardation were observed, with height and weight at approximately the 10th percentile (Fig. 1A and D). She was born with partial duplication of the thumb (preaxial polydactyly), which was corrected surgically; a postoperative scar was observed at the time of assessment (Fig. 1B and C). Electrocardiography (ECG) revealed no abnormalities. Multiple hyperpigmented skin lesions, including lentigines on the chest and back, were noted. Abdominal ultrasonography demonstrated normal hepatobiliary, pancreatic, splenic, and renal morphology, along with an infantile uterus without cervical edema. Echocardiography confirmed congenital heart disease characterized by multiple atrial septal defects with left-to-right shunting at the atrial level (Fig. 1C), with no evidence of hypertrophic cardiomyopathy.

Auditory rehabilitation outcomes after CI were excellent, with speech recognition scores of 96% for vowels, 96% for consonants, 100% for bisyllabic words, and 100% for short sentences (CAP/SIR score: 9/5). The patient underwent bimodal hearing rehabilitation, using a hearing aid in the right ear and a CI (CS-20A (TM); Nurotron, Hangzhou, China) in the left ear. Aided hearing thresholds were as follows: left ear—35, 40, 35, 20, 25, and 20 dB HL at 250 Hz, 0.5, 1, 2, 4, and 6 kHz, respectively; and right ear—35, 55, 60, 50, 50 and 50 dB HL at the corresponding frequencies.

Karyotype analysis revealed a normal 46XX chromosomal pattern. Trio-based WES identified a heterozygous missense variant c.1391G > C (p.Gly464Ala) in the PTPN11 gene (NM_002834) (Fig. 2b). Sanger sequencing confirmed the variant as de novo, being absent in unaffected parents. This variant has been previously reported as pathogenic in the ClinVar database (rs121918469) and meets the ACMG/AMP criteria for pathogenicity (PS2 + PS3_Strong + PS4 + PM2_Supporting + PP3).

Case 2

The proband was a 7-year-old boy (height 121 cm; weight 22 kg) with bilateral SNHL (Fig. 1E–H). There was no family history of hearing loss or other genetic disorders. He presented with multiple pigmented nevi distributed over the face and body, consisting of numerous lesions measuring 1.5 mm to 2 cm in diameter, round or elongated in shape, and yellowish to brownish-black in color. Additional features included low-set, posteriorly rotated ears. Physical examination revealed a normal hairline, normal spinal alignment, and no detectable cardiac murmurs. A single transverse palmar crease (simian crease) was observed on the right hand (Fig. 1H), along with a high-arched palate (Fig. 1K). The patient was born at full term via vaginal delivery with macrosomia (birth weight: 4,250 g). His younger brother, also born at term, had intrauterine growth restriction (birth weight: 2 kg) but exhibited normal hearing.

Diagnostic evaluations revealed a sinus rhythm with sinus arrhythmia on ECG, a chest X-ray without significant abnormalities, and ultrasound imaging exhibiting a hypoechoic chest wall lesion consistent with post-treatment lymphangioma changes. Abdominal ultrasound demonstrated splenomegaly with preserved morphology and no genital anomalies (cryptorchidism had been surgically corrected). Echocardiography confirmed normal cardiac anatomy and hemodynamics. On June 10, 2024, the patient underwent ultrasound-guided intralesional bleomycin injection for thoracic lymphangioma management.

Bilateral sequential cochlear implantation (CI; Cochlear™ CI512 with CP910 processors, Cochlear Ltd., Sydney, Australia) achieved aided hearing thresholds of 30–40–30–25–30 dB HL in the left ear and 25–35–30–25–20 dB HL in the right ear across frequencies from 250 Hz to 6 kHz. Postoperative auditory rehabilitation outcomes were excellent: speech recognition scores were 100% for vowels, 96% for consonants, 96% for bisyllabic words, and 100% for short sentences, with CAP/SIR scores of 9/5.

Karyotype analysis revealed a normal 46XY chromosomal pattern. Trio-based whole-exome sequencing (WES) identified a heterozygous missense variant, c.836A > G (p.Tyr279Cys), in the PTPN11 gene (Fig. 2b, Table 3). Sanger sequencing confirmed the variant as de novo, as it was absent in both unaffected parents. The p.Tyr279Cys substitution has been reported in the literature to be one of the most common alleles associated with LEOPARD syndrome (PMID: 21,339,643, 38,674,380). It is classified as a pathogenic or likely pathogenic variant in the ClinVar database (rs121918456) and meets the ACMG criteria for pathogenicity (PS2 + PS3_Strong + PS4 + PM2_Supporting + PP3).

Table 3.

Genotype and phenotype of patients with PTPN11 variants

Family ID	Gene symbol	Chromosome location	Exon	Domain	Reference mRNA	Genotype (nucleotide change)	Genotype (amino acid change)	dBSNP	Clinvar pathogenicity	Inheritance mode	Germline variant	Phenotype
Case 1	PTPN11	chr12:112,926,258	Exon 12	PTP	NM_002834	c.1391G > C	p.Gly464Ala	rs121918469	Pathogenic	AD	De nova	NS-ML
Case 2	PTPN11	chr12:112,910,827	Exon 7	PTP	NM_002834	c.836A > G	p.Tyr279Cys	rs121918456	Pathogenic/likely pathogenic	AD	De nova	NS-ML
Case 3	PTPN11	chr12:112,926,890	Exon 13	PTP	NM_002834	c.1510A > G	p.Met504Val	rs397507547	Pathogenic	AD	De nova	NS
Case 4	PTPN11	chr12:112,915,524	Exon 8	PTP	NM_002834	c.923A > G	p.Asn308Ser	rs121918455	Pathogenic	AD	De nova	NS

Case 3

The proband was a 17-year-old female who was diagnosed with bilateral severe SNHL at the age of 2 years and subsequently underwent auditory rehabilitation with bilateral hearing aids. She presented with short stature (height at the 3rd percentile) and ocular hypertelorism. Comprehensive cardiac evaluation, ECG and echocardiography, revealed no structural heart defects or hypertrophic cardiomyopathy. Neurodevelopmental and cognitive assessments indicated no intellectual disability. CI was significantly delayed because her parents, motivated by a desire to protect their child, chose to limit her social interactions and declined further medical interventions during childhood and adolescence. Her auditory and speech performance scores were 5 and 3 on the CAP and the SIR scales, respectively.

Karyotype analysis revealed a normal 46XX chromosomal pattern. Trio-based whole-exome sequencing identified a heterozygous missense variant, c.1510A > G (p.Met504Val), in the PTPN11 gene (Fig. 2b, Table 3). Sanger sequencing confirmed the variant as de novo, absent in both unaffected parents. This variant is classified as pathogenic in the ClinVar database (rs397507547) and meets the ACMG criteria for pathogenicity (PS2 + PS3 + PS4_Moderate + PM2_Supporting + PP3).

Case 4

The proband was a 4-year-old boy with bilateral SNHL (Fig. 1J and L–N). Clinical examination revealed prominent ears that were low-set and posteriorly rotated (Fig. 1J), with a normal palatal arch. Skeletal anomalies included rib flaring and pectus carinatum, whereas the hands were structurally normal. His medical history was notable for feeding difficulties during infancy, gross motor delay, hypertonia (unable to lift head at 5 months), and overall neurodevelopmental lag with normal Intellectual ability; independent walking was achieved at 17 months. Developmental assessment using the Gesell Developmental Schedule on January 13, 2025, demonstrated age-appropriate gross motor, fine motor, and adaptive language skills. Growth retardation persisted, with height and weight at the 3rd percentile (Fig. 1N).

Cardiac evaluation by echocardiography revealed no structural abnormalities but identified trace left-to-right atrial shunting, suggestive of a patent foramen ovale (Fig. 1M). Cervical ultrasound exhibited bilateral lymph nodes without edema. Hepatobiliary, pancreatic, splenic, renal, testicular, and epididymal structures were unremarkable. Thyroid function testing indicated mildly elevated thyroid stimulating hormone levels (4.710 μIU/mL; reference upper limit: 4.2 μIU/mL), whereas coagulation parameters were normal. Spinal imaging demonstrated normal alignment of the cervical, thoracic, and lumbosacral vertebrae, without evidence of scoliosis or osseous anomalies.

At the 3-year postoperative follow-up, audiological evaluation demonstrated speech recognition scores of 96% for vowels, 88% for consonants, 100% for bisyllabic words, and 95% for short sentences, with CAP/SIR scores of 8 and 5, respectively. The patient underwent left-sided CI (Cochlear™ Nucleus® 6) with bimodal hearing rehabilitation using a hearing aid in the contralateral ear. Aided thresholds were 35–40–35–40–35 dB HL in the left ear and 60–70–70–80–80 dB HL in the right ear across frequencies from 250 Hz to 6 kHz.

Karyotype analysis revealed a normal 46XY chromosomal pattern. Trio-based WES identified a de novo heterozygous missense variant, c.923A > G (p.Asn308Ser), in the PTPN11 gene, which was confirmed by Sanger sequencing (Fig. 2b, Table 3). This variant has been previously reported in ClinVar (rs121918455) and is classified as pathogenic according to ACMG criteria (PS2 + PS4 + PM2_Supporting + PP3) (Tables 1 and 2).

Electrophysiological results

Figure 3 illustrates the EABR waveforms elicited from the apical electrode in Cases 1, 2, and 4. High-quality EABR waveforms were obtained in all three patients, each achieving a Gibson score of 3, reflecting robust neural synchrony and excitation and aligning with favorable subjective auditory and speech outcomes. Detailed postoperative EABR evaluation results for these three CI recipients with PTPN11 variants are provided in Table 4, demonstrating well-differentiated, mature waveforms accompanied by high Gibson scores and favorable slope values.

Fig. 3.

Electrically evoked auditory brainstem response (EABR) waveforms elicited from the apical electrode in Cases 1, 2, and 4

Table 4.

Postoperative electrophysiological results (apical electrode selected)

EABR measure	Case1 NS-ML	Case2 NS-ML	Case 3 NS	Case 4 NS
EABR eV threshold (nC)	14.6	11.65	NA	13.94
EABR eV slope	0.28	0.036	NA	0.06
EABR eV Gibson Score	3	3	NA	3

EABR electrically evoked auditory brainstem response, NA not available, eV evoked voltage, nC nanoCoulombs

Discussion

Germ-line PTPN11 gene variants are responsible for NS and NS-ML syndrome. NS-ML shares substantial phenotypic overlap with NS—both are characterized by variable craniofacial dysmorphism, cardiac defects, growth retardation, developmental delay, cutaneous abnormalities, sensorineural deafness, lymphatic malformations, and bleeding or coagulation disorders [13, 14]. However, NS-ML is distinguished by its hallmark features of ML or café-au-lait spots (CLSs) and occurs much less frequently than NS [15]. Comprehensive molecular evaluation and long-term clinical follow-up are essential for accurate diagnosis and differential diagnosis in patients with borderline or overlapping clinical features. Although the precise pathophysiology of SHP-2 variant-driven NS and NS-ML remains uncertain, recent studies imply that ERK1/2 hyperactivation plays a pivotal role in NS pathogenesis [16]. NS-associated gain-of-function SHP-2 mutants enhance phosphatase activity and disrupt autoinhibitory regulation, resulting in hyperactivation of the RAS/MAPK signaling pathway [16–18]. In contrast to the signal-enhancing effect of SHP-2 on RAS/MAPK activation observed in NS, variants causing NS-ML may exert a dominant-negative effect on the wild-type protein. [19] These SHP-2 variants have been reported to reduce catalytic activity while simultaneously increasing binding affinity for upstream activators and/or stabilizing the protein in its open conformation [19]. Recent studies indicate that PTPN11-associated NS-ML may result from the combined dysregulation of the RAS/MAPK and the PI3K/AKT pathways [20]. However, findings from zebrafish models imply that certain developmental abnormalities observed in NS and NS-ML may not stem exclusively from RAS/MAPK pathway dysregulation. Instead, SHP-2 variants associated with these disorders may perturb signal transduction through distinct, non-synergistic mechanisms, producing highly similar phenotypic manifestations.

This study identified four PTPN11 missense variants associated with NS or NS-ML. The c.1391G > C (p.Gly464Ala) and c.836A > G (p.Tyr279Cys) variants were associated with NS-ML, whereas c.1510A > G (p.Met504Val) and c.923A > G (p.Asn308Ser) were identified in patients with NS [21, 22]. All four variants have been previously reported. Each family exhibited an autosomal dominant de novo inheritance pattern. Point variants in PTPN11 account for approximately 50% of NS cases and nearly 90% of NS-ML cases. According to the Human Gene Variant Database, 154 pathogenic PTPN11 variants have been reported, of which 142 are causative of NS. These include one splicing variant, nine frameshift variants, two nonsense variants, and a predominance of missense variants (n = 130). In contrast, 12 variants are specific to NS-ML. Most NS-associated variants affect amino acid residues located at the interface between the N-SH2 and PTP domains, disrupting autoinhibitory interactions. Notably, all NS-ML-associated variants are confined to the PTP domain. Approximately 85% of NS-ML cases involve heterozygous missense variants located in exons 7, 12, or 13 (Fig. 2). Additionally, a single amino acid deletion was reported in a patient with severe neonatal NS who later developed juvenile myelomonocytic leukemia [23]. However, data on other variant types remain limited.

In our cohort, the N308S variant affected residues that do not directly contribute to the N-SH2/PTP domain interaction or catalytic activity but play a structural role in maintaining the overall integrity of the PTP domain [5]. In contrast, the M504V variant interacted with residues involved in the catalytic process. Molecular dynamics simulations have demonstrated that Y279C, located within the PY loop, defines the depth of the catalytic site and contributes to substrate specificity [24]. The G464A substitution, situated in the P loop within the PTP signature motif, is essential for stabilizing the phosphotyrosine substrate-enzyme complex and involves highly conserved residues critical for phosphatase activity. Dysregulation of the RAS/MAPK and PI3K/AKT signaling pathways has been causally associated with the diverse clinical manifestations of NS and NS-ML. However, a definitive genotype–phenotype correlation linking specific PTPN11 variant types to the clinical variability observed in these syndromes remains unclear [25]. Clinical characteristics among patients demonstrate substantial phenotypic variability, even among individuals harboring the same genotype. Recently, Lee et al. reported distinct PTPN11 variants to be associated with variable penetrance, type and severity of hearing loss [25]. In particular, the p.Glu139Asp and p.Tyr279Cys variants are more frequently associated with severe-to-profound SNHL, whereas the p.Asn308Asp and p.Gly503Arg variants exhibit lower penetrance (approximately 11%) and milder expressivity of hearing loss. In our study, all four patients exhibited severe-to-profound SNHL with normal temporal bone morphology, craniofacial dysmorphism, and growth retardation. Notably, growth impairment appeared milder in the two NS-ML cases carrying heterozygous G464A or Y279C variants, whereas the patient with NS carrying the N308S variant (Case 4) demonstrated height at the 3rd percentile for age. It may be hypothesized that PI3K/AKT pathway hyperactivation in NS-ML could partially mitigate growth delay compared with NS [26]. Case 1 (G464A) presented with multiple atrial septal defects and left-to-right shunting at the atrial level, whereas case 4 exhibited a mild patent foramen ovale. None of the patients in this series exhibited obstructive hypertrophic cardiomyopathy. Scattered lentigines and ptosis were observed in case 1. Case 2 (Y279C) exhibited ML and CLSs, along with recurrent lymphangiomas requiring multiple surgical interventions. Cryptorchidism was diagnosed at 19 months of age in this patient and successfully corrected through early surgical management. Notably, SHP-2 variants associated with NS and NS-ML give rise to significantly diverse clinical features. In most instances, affected individuals initially present to clinical attention due to the most prominent manifestations. Consequently, management efforts often focus primarily on addressing the major or life-threatening features, sometimes overlooking concurrent signs of NS or NS-ML. Such oversight may lead to an incomplete therapeutic approach and potentially impact the long-term prognosis. Although the overall frequency of SNHL associated with PTPN11 variants is estimated to be < 20%, these variants typically cause congenital, severe-to-profound, nonprogressive hearing loss [8, 25]. A lack of timely intervention can lead to auditory deprivation, which may severely impair speech and language development. Therefore, regular audiological monitoring is essential for the early detection of hearing deterioration or related complications. An MDT approach is crucial for the comprehensive management of syndromic hearing loss. [11]

Experimental models have provided valuable insights into the otopathophysiology associated with PTPN11/SHP-2 variants. In murine cochleae, SHP-2 is expressed in spiral ganglion neurons, hair cells, and supporting cells of the inner ear. In zebrafish, ptpn11a knockdown and overexpression of mutant PTPN11 result in a significant reduction in both hair cells and supporting cells. [8] Moreover, Lee et al. demonstrated that shp2^N308D/þ mice exhibit impaired spatial learning and memory and defective synaptic plasticity, accompanied by increased ERK1/2 phosphorylation in the hippocampus. Clinically, studies of patients with profound hearing loss have shown that electrically evoked amplitude modulation following responses can still be elicited in those demonstrating correct perceptual responses, indicating preserved auditory nerve function despite severe cochlear pathology. These findings emphasize the intra-cochlear pathological consequences induced by SHP-2 variants, supporting the notion that CI can provide favorable auditory rehabilitation outcomes [25]. However, learning difficulties may potentially compromise CI performance. Our findings demonstrated favorable long-term auditory and speech outcomes, aligned with the limited previous studies on CI efficacy in PTPN11-related hearing loss [27, 28]. Notably, coagulation assessments, including multimer analysis for von Willebrand disease, are warranted in some patients with SHP-2-related variants, and appropriate perioperative strategies should be implemented to ensure CI safety. Early diagnosis and timely, evidence-based intervention are crucial for achieving optimal outcomes. Notably, in Case 4, the child attained age-appropriate development in motor, fine motor, and auditory-language skills following CI. These observations support the approach that early CI combined with comprehensive rehabilitation can facilitate holistic development, likely by enhancing auditory input, reducing cognitive load, and promoting multisensory integration. The family has recognized the benefits of the cochlear implant and has decided to proceed with contralateral cochlear implantation. The findings emphasize the value of multidisciplinary monitoring and integrated post-CI intervention strategies.

In addition, PTPN11-variant-related phenotypes in NS and NS-ML are highly heterogeneous. Beyond hearing loss, SHP-2 dysregulation contributes to a range of other pathological manifestations. Clinical management should address congenital anomalies as well as growth and motor development. The long-term prognosis of patients with PTPN11 variants depends largely on the type and severity of cardiac involvement. As recommended by cardiology guidelines, individuals with cardiac defects—particularly those presenting with ML—should undergo annual follow-up due to the increased risk of heart failure or sudden cardiac death. [29]

The molecular and pathophysiological mechanisms underlying the distinct effects of various PTPN11 variants on SHP-2-dependent signaling pathways remain an active area of investigation. In conclusion, our study emphasizes the role of CI in managing PTPN11-related SNHL. The outcomes of CI in patients with PTPN11 variants require validation in larger cohorts. Early CI is crucial to optimize language acquisition, and comprehensive multidisciplinary management should be emphasized in the care of patients with syndromic hearing loss.

Supplementary Information

Below is the link to the electronic supplementary material.

Authors' contributions

Concept and design: Yuan Li, Zhongyan Chen. Acquisition, analysis, or interpretation of data: Zhongyan Chen, Qingling Bi, Yong Lv, Yan Li, Wenjing Yang, Xiaoyu Xu, Yuan Li. Drafting of the manuscript: Yuan Li, Zhongyan Chen. Critical revision of the manuscript: Yuan Li, Zhongyan Chen, Qingling Bi; Clinical evaluation of syndromic hearing loss: Shufang Liu, Yanan Zhai, Guanghan Li, Jianfeng Liu, Yang Liu. All authors have approved the submitted version and have agreed both to be personally accountable for the author’s own contributions and to ensure that questions related to the accuracy or integrity of any part of the work.

Funding

National High Level Hospital Clinical Research Funding (No:2023-NHLHCRF-PY-02).

Declarations

Ethics approval and consent to participate

All procedures performed in studies involving human participants were in accordance with the ethical standards of the China-Japan Friendship Hospital Ethical Committee.

The Ethics Committee of the China-Japan Friendship Hospital approved the study protocol (approval No. 2023-KY-217–1). Informed consent was obtained from all individual participants involved in the study.

Consent for publication

Consents for publication were obtained from all participants.

Competing interests

The authors declare that they have no competing interests. The authors alone are responsible for the content and writing of this paper.