Is MYO7A p.Asn458Ser (c.1373A>G) pathogenic?

MYO7A p.Asn458Ser (c.1373A>G) is classified Uncertain significance in MYO7A (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-01-23). AlphaMissense: likely pathogenic (0.8708); Very rare (popmax 0.00448%, eas).

How common is MYO7A p.Asn458Ser (c.1373A>G) in the general population?

MYO7A p.Asn458Ser (c.1373A>G) is very rare (popmax 0.00448%, eas) (gnomAD).

What do computational predictors say about MYO7A p.Asn458Ser (c.1373A>G)?

AlphaMissense predicts likely pathogenic (score 0.8708) — an in-silico prediction, not a clinical call.

MYO7A p.Asn458Ser

c.1373A>G · VCV3627985

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.8708 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00448%, eas)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8708	likely pathogenic
REVEL	0.867	moderately pathogenic-leaning
SaProt	LLR -10.41	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 11	GERP 1.9, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 84 kb · p 0.0065 · regional, not allelic
Overall
CADD	23.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00448% East Asian · 2/44,626 alleles

Filtering AF 0.000957% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00079%

Overall 0.0015% 24/1,603,690 alleles · very rare exomes 21/1,451,482 · genomes 3/152,208 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00448%	22,313
South Asian	0.00226%	44,203
Remaining individualsnot grpmax-eligible	0.00161%	62,156
European (non-Finnish)	0.00153%	65,292
African / African-American	0.00134%	74,796

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.Asn458Ser
Coding: c.1373A>G
MANE Select: NM_000260
Type: single nucleotide variant
Location: chr11:77162149 (GRCh38)
Gene constraint: LOEUF 0.995 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73 · 1 PDB
Residue 458: the myosin motor domain; a UniProt-annotated variant site (in dfna11)

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

Similar variants

MYO7A p.Asn458Lys Uncertain significance ★★ ⚠ same residue
MYO7A p.Asn458Asp Likely pathogenic ★ same residue
MYO7A p.Asn458Ile Pathogenic ★ same residue
MYO7A p.Asn458= Likely benign ★ same residue
MYO7A p.Ala1288Pro Likely pathogenic ★★★ same type
MYO7A p.Arg1168Gln Pathogenic ★★★ ⚠ same type
MYO7A p.Arg1873Gln Pathogenic ★★★ ⚠ same type
MYO7A p.Arg395Cys Likely pathogenic ★★★ ⚠ same type

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-asn458ser (accessed [today's date]).

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