The spectrum of heart defects in the TRAF7-related multiple congenital anomalies-intellectual disability syndrome

Heterozygous missense variants in TRAF7 lead to various cancers when somatic and a multiple congenital anomalies-intellectual disability syndrome (MCA-IDS) when germline (1, 2). Variants are predominantly within the WD40 repeats and recurrent, suggesting specific alterations to the protein as the pathomechanism, as opposed to haploinsufficiency. Mishra-Gorur et al. (3) report three novel TRAF7 variants, p.Val142Met, p.Val442Met, and c.1998+2T>G, identified through analysis of exome data from 2,871 cases with congenital heart defects (CHDs). We disagree with several of the arguments put forward to support the pathogenicity of these variants. All were inherited from healthy parents, while non-penetrance of TRAF7 variants has not been previously reported in the MCA-IDS. Although absent from ExAC, p.Val142Met is found in 4/192,850 alleles in gnomAD v2 (a larger control dataset), indicating that it is unlikely to be the cause of the severe CHD in the patient in whom it was identified. The authors cite the high missense Z score of TRAF7 in ExAC as evidence that TRAF7 is susceptible to haploinsufficiency and therefore that their essential splice site variant is pathogenic through loss-of-function. However, the gnomAD probability of being loss-of-function intolerant of TRAF7 is 0.02, suggesting good tolerance to heterozygous loss-of-function variants in the general population, and arguing against c.1998+2T>G causing a CHD. One could propose that damaging missense variants in TRAF7 might increase susceptibility to CHDs, however, based on the frequency of missense variants with CADD score ≥26 in gnomAD (n = 42 from exomes, 33 from genomes), we estimate that the number of missense variants with the same CADD criterion identified by Mishra-Gorur et al. (2/2,871) is not more than expected in an equivalent-sized sample of controls (methodology of probability determination available on request).

The TRAF7-related MCA-IDS is composed of several recurrent features, including a typical facial gestalt, with >50 patients published. Apart from one paper (1), Mishra-Gorur et al. do not cite other studies describing this syndrome prior to 2023 (2, 4–7), including the largest study (45 patients), from 2020 (2). We present 21 new TRAF7-related MCA-IDS patients, in whom phenotypes are consistent with those previously published (Table 1). The three patients described in Mishra-Gorur et al. do not have typical clinical associations of the TRAF7 disorder, and their CHDs are variable; the patient with p.Val142Met has renal cysts and cardiac heterotaxy (suggestive of a ciliopathy), one has an isolated cardiopathy, and the patient with c.1998+2T>G has severe limb defects and truncus arteriosus (neither reported in TRAF7-related MCA-IDS). Based on the previous and new cohorts, we refine the frequencies of cardiac defects in the TRAF7 MCA-IDS (Table 2). Patent ductus arteriosus (PDA; not found in Mishra-Gorur et al.’s patients) is the most frequent feature, followed by septal and valvular defects.

Table 1.

Clinical features of a novel cohort of 21 patients with the TRAF7-related MCA-ID syndrome

Patient number	1	2	3	4	5	6	7	8	9	10	11
TRAF7 variant (c.)	1013A>T	1111C>T	1288A>G	1288A>G	1564T>C	1564T>C	1570C>T	1603A>G	1673C>T	1717G>T	1873C>T
TRAF7 variant (p.)	D338V	R371W	K430E	K430E	W522R	W522R	R524W	S535G	S558F	V573F	L625F
Inheritance	dn	un	dn	dn	un	i5	dn	dn	dn	dn	un
Age at LC	8 y	5 y	13 y	17 y	46 y	14 y	11 m	19 m	21 y	21 y	43 y
Sex	M	M	M	M	M	M	M	F	M	M	M
Clinical feature
ND abnormality	+	+	+	+	+	+	+	+	+	+	+
Hypotonia	+			+
Anomalies on brain scan										+
Abnormality of facial/skull shape	+						+		+
Hypertelorism		+		+							+
Blepharo or SPF	+					+			+	+	+
Ptosis	+			+			+		+	+
Micro- and/or retrognathia			+						+
Abnormality of external ear	+						+		+
Hearing impairment			+	+					+
Abnormality of hands or feet		+	+	+	+	+	+		+	+	+
Scoliosis or kyphosis			+			+				+
Short stature			+			+				+
FD or FTT				+
Cardiac anomalies
Quadricuspid AV
Bicuspid AV									+	+
Coarc of aorta
ASD
PFO
LSVC draining to CS
PDA							+		+
VSD									+
Aortic aneurysm									+
PAS

Patient number	12	13	14	15	16	17	18	19	20	21
TRAF7 variant (c.)	1873C>T	1873C>T	1958_1959​delinsTT	1964G>A	1964G>A	1964G>A	1964G>A	1964G>A	1964G>A	1964G>T
TRAF7 variant (p.)	L625F	L625F	R653L	R655Q	R655Q	R655Q	R655Q	R655Q	R655Q	R655L
Inheritance	i11	i11	dn	dn	dn	dn	dn	dn	dn	dn
Age at LC	8 y	4 y	7 y	9 y	24 y	10 y	18 m	9 y	18 m	14 m
Sex	M	F	F	F	F	F	M	F	F	F
Clinical feature
ND abnormality	+	+	+	+	+	+	+	+	+
Hypotonia			+			+		+	+
Anomalies on brain scan			+	+	+	+		+	+
Abnormality of facial/skull shape			+		+			+	+	+
Hypertelorism	+	+			+					+
Blepharo or SPF	+	+	+	+	+		+	+		+
Ptosis			+	+				+	+
Micro- and/or retrognathia			+			+	+		+
Abnormality of external ear			+	+	+					+
Hearing impairment			+	+		+		+
Abnormality of hands or feet	+	+	+			+				+
Scoliosis or kyphosis					+	+			+
Short stature	+				+	+		+
FD or FTT			+			+	+	+		+
Cardiac anomalies
Quadricuspid AV					+
Bicuspid AV
Coarc of aorta						+	+
ASD			+			+		+
PFO								+		+
LSVC draining to CS								+
PDA	+		+	+			+	+	+
VSD						+				+
Aortic aneurysm
PAS									+

All TRAF7 variants were identified by diagnostic testing in independent centers by whole-exome or genome sequencing (or an intellectual disability panel in one case), and patients were recruited to the present study via Genematcher or direct contact with the senior authors. Consent was obtained from the families for genetic analysis and for publication of anonymous data. Due to space limitations, only the most frequent phenotypes (or phenotype categories) are listed here, apart from cardiac anomalies, which are listed in detail. Major neurodevelopmental abnormalities consisted of global developmental delay, intellectual disability, or specific learning disabilities. Major abnormalities of the extremities consisted of contractures and finger/toe deviations. A complete list of HPO terms describing each patient is available from the authors on request. Mutation nomenclature is relative to RefSeq transcript NM_032271.3. LC, last consultation; dn, de novo; un, unknown; i5, inherited from patient 5; i11, inherited from patient 11; ND, neurodevelopmental; blepharo, blepharophimosis; SPF, short palpebral fissures; FD, feeding difficulties; FTT, failure to thrive; AV, aortic valve; coarc, coarctation; ASD, atrial septal defect; PFO, patent foramen ovale; PDA, patent ductus arteriosus; LSVC, left superior vena cava; CS, coronary sinus; VSD, ventricular septal defect; PAS, pulmonary artery stenosis.

Table 2.

Cardiac features in patients with the TRAF7-related MCA-ID syndrome

Reference	Tokita 2018 (N = 7)	Castill. 2020 (N = 42)	Acco. 2020 (N = 2)	Papro. 2021 (N = 2)	Chais. 2022 (N = 1)	Malin. 2022 (N = 1)	Colleran 2023 (N = 2)	Mish. 2023 (N = 3)	Present report (N = 21)
PDA (surgically repaired)	4 (2)	24 (10)	1	1	1		2		8 (6)
ASD	1	8		1			1	1	3
PFO		1						1	2
VSD	1	5	1			1			3
AV canal defect		1
Bicuspid aortic valve	2	6							2
Quadricuspid aortic valve									1
Mitral valve anomalies	2	3
SV pulmonary stenosis	1	1
Pulmonary atresia/stenosis	1							2	1
Bicuspid tricuspid valve				1
Tricuspid atresia								1
DORV	2					1
DOLV								1
L-loop transposition								1
Truncus arteriosus								1
Aortic coarctation	1		1						2
Hypoplastic aortic arch		1
Aortic aneurysm		1							1
Hypoplastic LV	2
Hypoplastic RV								1
Univentricle	1							1
Normal	1	9							6
Unknown		1							3

Only anomalies affecting the four chambers and great arteries are listed. Full details of references can be found in the main text, plus: Colleran et al (8). Although Castilla-Vallmanya et al., identified TRAF7 variants in 45 patients, N = 42 refers to the core cohort of patients harboring variants in the WD40 repeats. PDA, patent ductus arteriosus; ASD, atrial septal defect; PFO, patent foramen ovale; VSD, ventricular septal defect; AV, atrioventricular; DORV, double-outlet right ventricle; DOLV, double-outlet left ventricle; SV, supravalvular; LV, left ventricle; RV, right ventricle.

Although cardiac looping was abnormal upon traf7 knock-down in zebrafish and Xenopus in Mishra-Gorur et al., it was recently reported as normal in Traf7 knock-out mice (9). These mice display midgestational death due to endothelial dysplasia, which is intriguing given the frequency of PDA (a vessel wall closure anomaly) in the TRAF7 MCA-IDS.