The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
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Variant: NM_000260.4(MYO7A):c.1849T>C (p.Ser617Pro)

CA6197628

438172 (ClinVar)

Gene: MYO7A
Condition: nonsyndromic genetic deafness
Inheritance Mode: Autosomal recessive inheritance
UUID: 91d8a5fd-ca4f-426d-9b06-68e7858e7d7e

HGVS expressions

NM_000260.4:c.1849T>C
NM_000260.4(MYO7A):c.1849T>C (p.Ser617Pro)
NC_000011.10:g.77172799T>C
CM000673.2:g.77172799T>C
NC_000011.9:g.76883845T>C
CM000673.1:g.76883845T>C
NC_000011.8:g.76561493T>C
NG_009086.1:g.49536T>C
NG_009086.2:g.49554T>C
ENST00000409709.9:c.1849T>C
ENST00000669443.1:c.213T>C
ENST00000409619.6:c.1816T>C
ENST00000409709.7:c.1849T>C
ENST00000409893.5:c.1849T>C
ENST00000458637.6:c.1849T>C
ENST00000620575.4:c.1849T>C
NM_000260.3:c.1849T>C
NM_001127179.2:c.1849T>C
NM_001127180.1:c.1849T>C
NM_001127180.2:c.1849T>C
NM_001369365.1:c.1816T>C

Likely Pathogenic

Met criteria codes 3
PP1_Strong PP3 PM3
Not Met criteria codes 7
BS1 BP4 BP1 BA1 PP4 PP2 PM2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Hearing Loss Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for CDH23, COCH, GJB2, KCNQ4, MYO6, MYO7A, SLC26A4, TECTA and USH2A Version 2

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The c.1849T>C variant in MYO7A is a missense variant predicted to cause substitution of serine by proline at amino acid 617 (p.Ser617Pro). The highest population minor allele frequency in gnomAD v4 is 0.00009496 (8/84244 alleles) in the South Asian population (PM2_Supporting, BS1, and BA1 are not met). The computational predictor REVEL gives a score of 0.922, which is above the threshold of 0.7, evidence that correlates with impact to MYO7A function (PP3). This variant has been detected in 3 individuals with nonsyndromic hearing loss. Of those individuals, 2 were compound heterozygous for the variant and a pathogenic or likely pathogenic variant and both of those were confirmed in trans by parental testing (c.20G>T [p.Gly7Val], c.1258A>T [p.K420*], 2 PM3 points, PMIDs: 30303587, 33187236). One individual was homozygous for the variant (0.5 PM3 points, PMIDs: 27344577, 33671976) (PM3). The variant has been reported to segregate with nonsyndromic hearing loss in 7 affected family members from 3 families (PP1_Strong; PMIDs: 27344577, 30303587, 33187236, 33671976). This variant has also been detected in 1 individual with Usher syndrome, with a second variant c.4838delA (p.Asp1613ValfsTer32) without phase confirmation (PMIDs: 28041643, 32581362). In summary, this variant meets the criteria to be classified as likely pathogenic for autosomal recessive hearing loss based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP: PP1_S, PM3, PP3. (Hearing Loss VCEP specifications version 2; 4/22/2024). As cases have been observed with both nonsyndromic hearing loss and Usher syndrome and genotype-phenotype correlation is currently unclear, individuals should be evaluated for both conditions.
Met criteria codes
PP1_Strong
The variant has been reported to segregate with nonsyndromic hearing loss in 7 affected family members from 3 families (PP1_Strong; PMIDs: 27344577, 30303587, 33187236, 33671976).
PP3
The computational predictor REVEL gives a score of 0.922, which is above the threshold of 0.7, evidence that correlates with impact to MYO7A function (PP3).
PM3
This variant has been detected in 3 individuals with nonsyndromic hearing loss. Of those individuals, 2 were compound heterozygous for the variant and a pathogenic or likely pathogenic variant and both of those were confirmed in trans by parental testing (c.20G>T [p.Gly7Val], c.1258A>T [p.K420*], 2 PM3 points, PMIDs: 30303587, 33187236). One individual was homozygous for the variant (0.5 PM3 points, PMIDs: 27344577, 33671976) (PM3).
Not Met criteria codes
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
Not applicable
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
This variant has also been detected in 1 individual with Usher syndrome (HL and RP), with a second variant c.4838delA (p.Asp1613ValfsTer32) without phase confirmation (PMIDs: 28041643, 32581362). This is not scored for PP4 due to being curated for NSGHL.
PP2
Not applicable
PM2
The highest population minor allele frequency in gnomAD v4 is 0.00009496 (8/84244 alleles) in the South Asian population (PM2_Supporting, BS1, and BA1 are not met).
Approved on: 2024-06-28
Published on: 2024-06-28
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