Is MYO7A p.Ile376Val (c.1126A>G) pathogenic?

MYO7A p.Ile376Val (c.1126A>G) is classified Conflicting classifications of pathogenicity in MYO7A (ClinVar, Conflicting submitters, 7 submitters; last evaluated 2026-01-28). AlphaMissense: ambiguous (0.3595); Ultra-rare (popmax 0.0399%, nfe); Associated with Inborn genetic diseases.

What condition is associated with MYO7A p.Ile376Val (c.1126A>G)?

MYO7A p.Ile376Val (c.1126A>G) is associated with Inborn genetic diseases, Usher syndrome type 1, autosomal recessive nonsyndromic hearing loss 2 (ClinVar).

How common is MYO7A p.Ile376Val (c.1126A>G) in the general population?

MYO7A p.Ile376Val (c.1126A>G) is ultra-rare (popmax 0.0399%, nfe) (gnomAD).

What do computational predictors say about MYO7A p.Ile376Val (c.1126A>G)?

AlphaMissense predicts ambiguous (score 0.3595) — an in-silico prediction, not a clinical call.

MYO7A p.Ile376Val

c.1126A>G · rs368716988 · VCV178478

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 7 submitters

AlphaMissense

ambiguous

0.3595 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0399%, nfe)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3595	ambiguous
REVEL	0.277	benign-leaning
SaProt	LLR -5.22	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.2	GERP 0.53, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 84 kb · p 0.0065 · regional, not allelic
Overall
CADD	23.4	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0399% European (non-Finnish) · 464/1,164,026 alleles

Filtering AF 0.0369% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0356%

Overall 0.0307% 486/1,580,772 alleles · ultra-rare exomes 459/1,428,562 · genomes 27/152,210 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0399%	2,509
Remaining individualsnot grpmax-eligible	0.0196%	5,106
African / African-American	0.0121%	8,231
Admixed American	0.0018%	55,614

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: MYO7A
Protein: p.Ile376Val
Coding: c.1126A>G
MANE Select: NM_000260
dbSNP: rs368716988
Type: single nucleotide variant
Location: chr11:77160208 (GRCh38)
Gene constraint: LOEUF 0.995 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73 · 1 PDB
Residue 376: the myosin motor domain

Full MYO7A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Usher syndrome type 1 autosomal recessive nonsyndromic hearing loss 2 autosomal dominant nonsyndromic hearing loss 11

Similar variants

MYO7A p.Ile376Thr Uncertain significance ★ ⚠ same residue
MYO7A p.Ile376= Likely benign ★ same residue
MYO7A p.Ala1288Pro Likely pathogenic ★★★ same condition
MYO7A p.Arg1168Gln Pathogenic ★★★ ⚠ same condition
MYO7A p.Arg1873Gln Pathogenic ★★★ ⚠ same condition
MYO7A p.Arg395Cys Likely pathogenic ★★★ ⚠ same condition
MYO7A p.Arg668Cys Pathogenic ★★★ same condition
MYO7A p.Arg853His Likely pathogenic ★★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/myo7a-p-ile376val (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown