Is MYO7A p.Gly7Val (c.20G>T) pathogenic?

MYO7A p.Gly7Val (c.20G>T) is classified Pathogenic/Likely pathogenic in MYO7A (ClinVar, Multiple submitters, 8 submitters; last evaluated 2026-05-15). AlphaMissense: likely pathogenic (0.9301); Ultra-rare (popmax 0.0156%, sas); Associated with Usher syndrome.

What condition is associated with MYO7A p.Gly7Val (c.20G>T)?

MYO7A p.Gly7Val (c.20G>T) is associated with Usher syndrome, intellectual disability, Usher syndrome type 1 (ClinVar).

How common is MYO7A p.Gly7Val (c.20G>T) in the general population?

MYO7A p.Gly7Val (c.20G>T) is ultra-rare (popmax 0.0156%, sas) (gnomAD).

How is Usher syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about MYO7A p.Gly7Val (c.20G>T)?

AlphaMissense predicts likely pathogenic (score 0.9301) — an in-silico prediction, not a clinical call.

MYO7A p.Gly7Val

c.20G>T · rs781989117 · VCV562084

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

AlphaMissense

likely pathogenic

0.9301 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0156%, sas)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Usher syndrome

Computational evidence

Protein change
AlphaMissense	0.9301	likely pathogenic ✓ concordant with ClinVar
REVEL	0.937	strongly pathogenic-leaning
SaProt	LLR -15.00	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.4, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 84 kb · p 0.0065 · regional, not allelic
Overall
CADD	31.0	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 0.0156% South Asian · 14/89,464 alleles

Filtering AF 0.00945% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00758%

Overall 0.00087% 14/1,609,010 alleles · ultra-rare exomes 14/1,456,708 · genomes 0/152,302 · joint denominator

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.Gly7Val
Coding: c.20G>T
MANE Select: NM_000260
dbSNP: rs781989117
Type: single nucleotide variant
Location: chr11:77142710 (GRCh38)
Gene constraint: LOEUF 0.995 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73 · 1 PDB

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

Disease context

Usher syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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

For Usher syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Worldwide)

Similar variants

MYO7A p.Gly7Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
MYO7A p.Gly7Trp Uncertain significance ★ ⚠ 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-gly7val (accessed [today's date]).

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