Is MYO7A p.Gly556Val (c.1667G>T) pathogenic?

MYO7A p.Gly556Val (c.1667G>T) is classified Likely pathogenic in MYO7A (ClinVar, No assertion criteria, 1 submitter). AlphaMissense: likely pathogenic (0.995); Absent from gnomAD v4.1; Associated with retinitis pigmentosa.

What condition is associated with MYO7A p.Gly556Val (c.1667G>T)?

MYO7A p.Gly556Val (c.1667G>T) is associated with retinitis pigmentosa (ClinVar).

How common is MYO7A p.Gly556Val (c.1667G>T) in the general population?

MYO7A p.Gly556Val (c.1667G>T) is absent from gnomAD v4.1 (gnomAD).

How is Retinitis pigmentosa inherited?

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

What do computational predictors say about MYO7A p.Gly556Val (c.1667G>T)?

AlphaMissense predicts likely pathogenic (score 0.995) — an in-silico prediction, not a clinical call.

MYO7A p.Gly556Val

c.1667G>T · rs527236085 · VCV143064

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.995 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

retinitis pigmentosa

Computational evidence

Protein change
AlphaMissense	0.995	likely pathogenic ✓ concordant with ClinVar · top 9% in MYO7A
REVEL	0.844	moderately pathogenic-leaning
SaProt	LLR -15.40	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 1.9, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 84 kb · p 0.0065 · regional, not allelic
Overall
CADD	23.8	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: MYO7A
Protein: p.Gly556Val
Coding: c.1667G>T
MANE Select: NM_000260
dbSNP: rs527236085
Type: single nucleotide variant
Location: chr11:77162965 (GRCh38)
Gene constraint: LOEUF 0.995 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73 · 1 PDB
Residue 556: the myosin motor domain

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

Disease context

retinitis pigmentosa — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Retinitis pigmentosa (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, Mitochondrial inheritance
Onset: Adolescent, Adult, Childhood
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

MYO7A p.Gly556Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
MYO7A p.Gly556= Likely benign ★ same residue
MYO7A p.Cys31Ter Pathogenic ★★ same condition
MYO7A p.Pro541Arg Uncertain significance ★★ ⚠ same condition
MYO7A p.Gly556fs Pathogenic ★ same residue
MYO7A p.Met262Arg Likely pathogenic ★ same condition
MYO7A p.Glu1095Lys Conflicting classifications of pathogenicity ★ ⚠ same condition
MYO7A c.3503+12G>A Likely benign ★ 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-gly556val (accessed [today's date]).

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