. 2016 Nov 10;6(1):3–17. doi: 10.1055/s-0036-1593840

Table 1. Human imprinting disorders, their underlying molecular causes and strategies for genetic testing.

Syndrome/OMIM#/population frequency	Imprinted domain	Clinical features	Known molecular causes	Underlying genetic/epigenetic change	Molecular genetic testing	Multiple imprinting defect
Beckwith-Wiedemann syndrome (BWS) OMIM#130650 1:13,700	11p15.5	Macroglossia, macrosomia, abdominal wall defects, visceromegaly, neonatal hypoglycemia, hemihyperplasia. Increased risk (7.5%) for childhood tumors. The same molecular alterations as in BWS are found in approximately one-third of patients with isolated hemihyperplasia (OMIM: #235000). Incidence of BWS is increased in children born to subfertile couples and couples using ART, due to increased frequency of LOM at ICR2. ¹³	Overexpression of paternally expressed growth promoting gene IGF2. Loss of expression/function of maternally expressed growth suppressor gene CDKN1C.	• LOM at ICR2–50–60% (∼2% due to micro CNVs) ⁵⁴ • GOM at ICR1 −5–10% (∼35% due to micro CNVs, rarely point mutations in ICR1 OCT-binding sites) ¹⁰ ⁵⁴ • UPD (11) pat (usually segmental, can be mosaic)-20% • Loss of function mutations on maternal CDKN1C allele −5% (40% in familial cases) ¹⁰ • 11p15.5 CNVs up to 8.4% ⁵⁴ • Cytogenetically visible alterations including paternal duplications and maternal balanced inversions and translocations involving 11p15.5 <1% ¹³ • Unknown ∼20% ¹³	Sporadic cases: • MS-MLPA of 11p15.5 locus • If MS-MLPA is positive without CNV, UPD analysis to delineate molecular mechanism • If MS-MPLA is negative, CDKN1C sequencing Familial cases: • CDKN1C sequencing • ICRs microdeletion/ microduplication testing If all tests are negative, consider testing in another cell type: skin fibroblasts, buccal cells, tumor biopsy, due to possibility of mosaic UPD or methylation defect. ¹³ Karyotype analysis can be initiated at the same time as molecular testing. ¹³	MID found in ∼26% of BWS cases with isolated ICR2 LOM. ¹⁵ Maternal NLRP2 and NLRP5 mutations are found in several families with BWS and MID. ²² ²⁶ Possible association with ART. ¹⁰
Russell-Silver (RSS) OMIM#180860 1:10,000–30,000	11p15.5 7p11.2-p13 7q31	IUGR, postnatal growth retardation with normal head circumference (relative macrocephaly); failure to thrive, low BMI, typical facial features with triangular facies characterized by broad forehead and narrow chin, limb and body asymmetry present in > 50% of cases. Risk for developmental delay and learning difficulties.	Loss of expression of paternally expressed growth promoting gene IGF2 and/or overexpression of maternally expressed growth suppressor gene CDKN1C 11p15.5. Altered expression of imprinted genes on chromosome 7p11.2-p13 and 7q31. Rare genomic and eigenomic alterations at other loci. ³⁵ ⁶⁴ ⁶⁵ ⁶⁶ ⁶⁷	• LOM at ICR1 at 11p15.5 −35–45% • 11p15.5 maternal duplications −1–2% • UPD (11) mat –rare • Gain of function mutation of maternal allele of CDKN1C – one RSS family ⁶⁸ • UPD(7) mat- including segmental UPD of 7q-10% • Maternal duplications of 7p11.2-p13- rare • Other (sub)-microscopic imbalances −1% • Unknown ∼48% ⁶⁹ • Other rare causes: LOM at IG-DMR and the MEG3- DMR at the 14q32.2, ⁶⁴ ⁶⁶ HMGA2 mutation, ⁶⁵ gain of methylation at IGF2R at 6q25.3. ³⁵	• MS-MLPA of 11p15.5 locus • If MS-MLPA is positive without CNV, UPD analysis to delineate molecular mechanism at 11p15.5 • If MS-MLPA is negative, UPD 7 testing • If both 11p15.5 and UPD 7 tests are negative - array CGH ⁶⁹ If all tests are negative, consider methylation testing in another cell type: skin fibroblasts, buccal cells, due to possibility of mosaic LOM at ICR1 ⁶⁹	MID is found in ∼10% of RSS patient with ICR1 hypomethylation. ¹⁵ Maternal NLRP5 mutation is found in several families with SRS and MID. ²⁶
IMAGe syndrome OMIM #614732 Unknown (rare)	11p15.5	IUGR, metaphyseal dysplasia, adrenal hypoplasia congenita, and genitourinary abnormalities (in males)	Gain of function of maternally expressed growth suppressor gene CDKN1C .	• Gain of function missense mutations on maternally inherited allele of CDKN1C . All pathogenic mutations described to date are located within a five amino acid region of the PCNA -binding domain. ⁷⁰ ⁷¹	Targeted mutation testing of the PCNA-binding domain or sequencing of the entire CDKN1C gene.	Not applicable
Prader-Willi syndrome (PWS) OMIM #176270 1:17,500, Prader-Willi like syndrome (PWLS) OMIM#615547 caused by paternal MAGEL2 mutations	15q11-q13	Hypotonia and feeding difficulties in early infancy, global developmental delay, overeating, obesity, mild intellectual disability, hypogonadism, and specific behavioral problems including temper tantrums, stubbornness, manipulative behavior, obsessive-compulsive characteristics.	Loss of paternally expressed genes at 15q11-q13: protein-coding MKRN3, MAGEL2, NDN, NPAP1, SNURF-SNRPN and a cluster of six snoRNA genes. No single gene responsible for PWS was identified, however paternal deletions of SNORD116 snoRNAs ⁷² ⁷³ and paternal truncating mutations in MAGEL2 ⁷⁴ were reported in small proportion of PWS and PWS-like cases.	• Paternal deletion of 15q11-q13 -75–80%: a) Class I (BP1–BP3)∼30% b)Class II (BP2-BP3) ∼60% c) Atypical deletions ∼8% ⁷⁵ d) Detectable chromosomal rearrangement resulting in 15q11-q13 deletion −1% • UPD(15) mat −20–25% • Imprinting defect-1%: a) Idiopathic GOM −85–90% b) Paternal ICR microdeletions deletions −10–15% • Balanced chromosomal rearrangement at 15q11–13 < 1% ⁷⁶ • Mutations on paternal allele of MAGEL2 < 1% ⁷⁴	• MS-MLPA of 15q11-q13 will detect all mechanisms except some atypical small deletions and MAGEL2 mutations. • If MS-MLPA test is positive without CNV, UPD analysis to delineate molecular mechanism. • If MS-MLPA test is negative, PWS diagnosis is very unlikely, however SNORD116 copy number testing and MAGEL2 sequencing can be considered.	Single patient with clinical features of PWS and BWS, and LOM consistent with BWS and AS, and several other imprinted loci. ⁷⁷
Angelman (AS) OMIM#105830 1:16,000	15q11-q13	Severe developmental delay/intellectual disability, severe speech impairment, gait ataxia/tremulousness of the limbs, unique behavior with an inappropriate happy demeanor that includes frequent laughing, smiling, and excitability. Seizures and microcephaly are common.	Loss of expression or function of maternally expressed gene UBE3A in the brain ( UBE3 A expression is restricted to maternal allele in brain and is biallelic in other tissues).	• Maternal deletions of 15q11–13 −70–75%: a) Class I (BP1-BP3) ∼ 40% b) Class II (BP2-BP3 ∼50% c) Longer deletions ∼10% ⁷⁸ • UPD (15) pat −3–7% • Imprinting defect −2–3%: a)Maternal ICR microdeletions-10–15% b) Idiopathic LOM at ICR −85–90% (approximately one-third exhibit somatic mosaicism) • Mutations on maternal allele of UBE3A ∼10% Deletions of maternal allele of UBE3A < 1% • Balanced chromosome rearrangements <1% • Unknown-∼10% ⁷⁹ ⁸⁰	• MS-MLPA of 15q11-q13 will detect all mechanisms except UBE3A mutations. • If MS-MLPA is positive without CNV, UPD analysis to delineate molecular mechanism. • If MS-MLPA is negative, UBE3A sequencing. • Somatic mosaicism for LOM at ICR was reported; ⁸¹ thus, testing of another cell type can be considered if methylation test is negative.	Not reported
Duplication 15q11-q13 syndrome OMIM: #608636 1:12,000	15q11-q13	Autism spectrum disorder, hypotonia, developmental delay, intellectual disability, seizures	Unknown, but likely overexpression of UBE3A and nonimprinted genes located within duplicated region, such as GABA receptors.	• Maternal tandem duplication/triplication of PWS/AS critical region or supernumerary marker chromosome 15. The pathogenecity of paternal gains is uncertain. ⁵⁷	• CMA, karyotype, methylation-based test to determine parent of origin.	Not applicable
Transient diabetes mellitus type 1 (TNDM1) OMIM #601410 1:400,000	6q24	IUGR and neonatal hyperglycemia resolving by 18 months. ∼50% of cases have relapse of diabetes in adolescence or early adulthood. Macroglossia and umbilical hernia can be present. Patients with TNDM1-MID and ZFP57 mutation can have structural brain anomalies, cardiac malformations, and developmental delay.	Overexpression of paternally expressed genes PLAGL1 and HYMA1 . PLAGL1 is transcription factor and tumor suppressor gene. HYMA1 is noncoding RNA.	• UPD (6) pat −40% • Paternal duplications of 6q24 (majority submicroscopic)- 32% • Idiopathic LOM at maternal TNDM1 DMR- 28%. ¹⁴	• MS-MLPA at 6q24 will detect all mechanisms. • If MS-MLPA is without CNV positive, UPD analysis test to delineate molecular mechanism. • If no UPD or CNV detected, ZFP57 sequencing.	MID found in ∼60% of TNDM1 patients with primary TNDM1 DMR LOM. More than half of MID cases are caused by homozygous or compound heterozygous ZFP57 mutation. ¹⁹
Temple syndrome/UPD maternal 14 OMIM #616222 Unknown (rare)	14q32	Prenatal and postnatal growth restriction, neonatal hypotonia, feeding difficulty, and early puberty. In infancy can resemble PWS ⁸² or RSS. ⁶⁶	Reduced expression of paternally expressed genes DLK1 and RTL1 .	• UPD(14)mat −70–80% • Paternal deletions 14q32.2∼10% • LOM at IG-DMR and/or MEG3 DMR ∼12% • Paternal microdeletions of IG-DMR ≤2% ⁴²	• MS-MLPA testing at 14q32. • If MS-MLPA is positive without CNV, UPD analysis to delineate molecular mechanism	Not reported
Kagami-Ogata Syndrome(KOS)/UPD paternal 14 OMIM #608149 Unknown (rare)	14q32	Facial abnormality, small bell-shaped thorax, abdominal wall defects, placentomegaly, and polyhydraminos.	Overexpression of paternally expressed gene RTL1. Maternally expressed RTL1 antisense transcript (RTL1-as) is a micro-RNA down-regulating RTL 1 expression in trans, thus maternal deletions involving RTL1 and RTL1- as result in mild KOS phenotype even if RTL1 is present in single copy. ⁸³	• UPD(14) pat-65–70% • Maternal deletions 14q32.2–15–20% • GOM at IG-DMR and/or MEG3 DMR 10–15% • Maternal ICR microdeletions (IG-DMR and/or MEG3 DMR) < 5% ⁴² ⁸⁴ Note: MEG3 DMR is unmethylated in placenta and cannot be used for prenatal diagnosis in CVS.	• MS-MLPA testing at 14q32. • If MS-MLPA is positive without CNV, UPD analysis to delineate molecular mechanism.	Not reported
Pseudo-hypoparathyroidism type 1a (PHP1a) OMIM #103580 1:150,000 for PHP1a, PHP1b and PPHP (AHO without PHO)	20q13.3	AHO: short stature, round face, subcutaneous calcification or ossifications, brachymetacarpia, and cognitive impairment. + End-organ resistance to PTH, TSH, and gonadotropins.	AHO features are caused by constitutional 50% reduction of stimulatory G-protein subunit Gsα activity. Hormone resistance is caused by loss of function of Gsα in endocrine tissues (pituitary, thyroid, and ovary) with paternal imprinting (silencing) of Gsα.	• Loss of function mutations on maternal allele of Gsα (exons 1–13 of GNA S) – majority of cases. • Microdeletions of maternal alleles of Gsα- rare ⁸⁵ Inactivating mutations on paternal allele of Gsα cause AHO without hormone resistance.	• Sequencing of GNAS locus. • If negative, CNV analysis of GNAS .	Not applicable
Pseudo-hypoparathyroidism type 1b (PHP1b) OMIM #603233	20q13.3	End-organ resistance to PTH, TSH, and gonadotropins. Some PHP1b cases (based on molecular diagnosis) can manifest mild features of AHO. ⁸⁶	Loss of expression of Gsα in endocrine tissues (pituitary, thyroid, and ovary) with paternal imprinting (silencing) of Gsα.	• LOM at maternal GNAS1A DMR (sometimes accompanied by LOM at GNASXL/NESPAS and/or GOM at NESP55 DMRs)—majority of cases • UPD(20) pat –rare • In familial cases, LOM is associated with maternal deletions in cis at STX16 or NESP55 . ⁸⁷	• MS-MLPA testing at 20q13.3. • If MS-MLPA is positive without CNV, UPD analysis to delineate molecular mechanism. ⁸⁸ • Somatic mosaicism for methylation defect was observed, ⁸⁸ thus testing of another cell type can be considered in case of negative result.	∼12% of PHP1b cases with idiopathic methylation defects at GNAS locus exhibit MID. ¹⁵

Abbreviations: AHO, albright hereditary osteodystrophy; ART, assisted reproductive technologies; BMI, body mass index; BP, break point; CMA, chromosomal microarray; CNV, copy number variant; CVS, chorionic villus samples; DMR, differentially methylated region; GOM, gain of methylation; ICR, imprinting control region; IUGR, intrauterine growth restriction; LOM, loss of methylation; MID, multiple imprinting defect (methylation alterations at multiple ICRs); MS-MLPA, methylation-specific multiplex ligation-dependent probe amplification; PCNA, proliferating cell nuclear antigen; PTH, parathyroid hormone; snoRNA, small noncoding RNAs; SRO, smallest region of overlap; TSH, thyroid-stimulating hormone; UPD, uniparental disomy.

Note: Molecular genetic testing strategy described here is using MS-MLPA for simultaneous detection of copy number and methylation changes as first-tier test ( Fig. 4B ). For alternative strategy using methylation-based test without CNV analysis, refer to Fig. 4A .