Submissions for variant NM_005921.2(MAP3K1):c.934A>T (p.Met312Leu)

gnomAD frequency: 0.00020  dbSNP: rs376808920

Total submissions: 4

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Labcorp Genetics (formerly Invitae), Labcorp	RCV000648705	SCV000770526	likely benign	46,XY sex reversal 6	2024-07-26	criteria provided, single submitter	clinical testing
Genetic Services Laboratory, University of Chicago	RCV001816608	SCV002070518	uncertain significance	not specified	2020-03-31	criteria provided, single submitter	clinical testing
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	RCV000648705	SCV002766869	uncertain significance	46,XY sex reversal 6	2022-03-31	criteria provided, single submitter	clinical testing	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3B. Following criteria are met: 0101 - Gain of function is a known mechanism of disease in this gene and is associated with 46,XY sex reversal 6 (MIM#613762). Functional studies of missense variants observed in affected individuals have shown they increase phosphorylation of downstream products causing increased activation of the MAPK pathway (PMIDs: 24135036, 21129722, 30608580). (I) 0107 - This gene is associated with autosomal dominant disease. The condition associated with this gene is inherited in a sex limited manner; only individuals with a 46,XY karyotype are affected (PMID: 20301714). (I) 0115 - Variants in this gene are known to have variable expressivity. Intrafamilial and interfamilial variability have been reported, with individuals harbouring the same variants observed to have variable phenotypes, ranging from hypospadias to complete gonadal dysgenesis (PMIDs: 27899157, 12476449, 21129722). (I) 0200 - Variant is predicted to result in a missense amino acid change from methionine to leucine. (I) 0251 - This variant is heterozygous. (I) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v3) (2 heterozygotes, 0 homozygotes). (I) 0310 - Variant is present in gnomAD (v3) >=0.001 and <0.01 for a dominant condition (22 heterozygotes, 4 homozygotes). However, the four homozygotes and 17 heterozygotes had an XX karyotype and would therefore be expected to be unaffected carriers of 46,XY sex reversal. (I) 0502 - Missense variant with conflicting in silico predictions and high conservation. (I) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0803 - This variant has limited previous evidence of pathogenicity in unrelated individuals. This variant has been classified as likely pathogenic in four individuals in the literature with variable phenotypes including hypospadias, disorders of sex development, and complete gonadal dysgenesis (PMID: 27899157). However, two of these individuals also had a variant in another gene associated with DSD. This variant has also been classified as likely pathogenic, likely benign and as a VUS by clinical laboratories in ClinVar. (SP) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
Fulgent Genetics, Fulgent Genetics	RCV000648705	SCV005673532	uncertain significance	46,XY sex reversal 6	2024-01-03	criteria provided, single submitter	clinical testing