Is MYO7A p.Asn458Ile (c.1373A>T) pathogenic?

MYO7A p.Asn458Ile (c.1373A>T) is classified Pathogenic in MYO7A (ClinVar, Single submitter, 4 submitters; last evaluated 2022-04-25). AlphaMissense: likely pathogenic (0.9958); Absent from gnomAD v4.1; Associated with autosomal dominant nonsyndromic hearing loss 11.

What condition is associated with MYO7A p.Asn458Ile (c.1373A>T)?

MYO7A p.Asn458Ile (c.1373A>T) is associated with autosomal dominant nonsyndromic hearing loss 11 (ClinVar).

How common is MYO7A p.Asn458Ile (c.1373A>T) in the general population?

MYO7A p.Asn458Ile (c.1373A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MYO7A p.Asn458Ile (c.1373A>T)?

AlphaMissense predicts likely pathogenic (score 0.9958) — an in-silico prediction, not a clinical call.

MYO7A p.Asn458Ile

c.1373A>T · rs121965084 · VCV11863

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 4 submitters

AlphaMissense

likely pathogenic

0.9958 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

autosomal dominant nonsyndromic hearing loss 11

Computational evidence

Protein change
AlphaMissense	0.9958	likely pathogenic ✓ concordant with ClinVar · top 8% in MYO7A
REVEL	0.884	moderately pathogenic-leaning
SaProt	LLR -14.36	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	24.5	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.Asn458Ile
Coding: c.1373A>T
MANE Select: NM_000260
dbSNP: rs121965084
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

Disease context

autosomal dominant nonsyndromic hearing loss 11 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MYO7A p.Asn458Lys Uncertain significance ★★ ⚠ same residue
MYO7A p.Asn458Ser Uncertain significance ★★ ⚠ same residue
MYO7A p.Asn458Asp Likely pathogenic ★ same residue
MYO7A p.Asn458= Likely benign ★ same residue
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

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-asn458ile (accessed [today's date]).

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