Is MYO7A p.Asp1030= (c.3090C>T) pathogenic?

MYO7A p.Asp1030= (c.3090C>T) is classified Likely benign in MYO7A (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-07-29). Ultra-rare (popmax 0.0472%, sas); Associated with Usher syndrome type 1B.

What condition is associated with MYO7A p.Asp1030= (c.3090C>T)?

MYO7A p.Asp1030= (c.3090C>T) is associated with Usher syndrome type 1B (ClinVar).

How common is MYO7A p.Asp1030= (c.3090C>T) in the general population?

MYO7A p.Asp1030= (c.3090C>T) is ultra-rare (popmax 0.0472%, sas) (gnomAD).

MYO7A p.Asp1030=

c.3090C>T · rs782192026 · VCV991231

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0472%, sas)

Conditions

Usher syndrome type 1B

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -20	GERP -3.5
Overall
CADD	0.203	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0472% South Asian · 43/91,082 alleles

Filtering AF 0.036% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0321%

Overall 0.00372% 60/1,613,336 alleles · ultra-rare exomes 56/1,461,088 · genomes 4/152,248 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0472%	2,118
East Asian	0.0223%	4,486
African / African-American	0.00267%	37,515
European (non-Finnish)	0.000424%	235,973

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.Asp1030=
Coding: c.3090C>T
MANE Select: NM_000260
dbSNP: rs782192026
Type: single nucleotide variant
Location: chr11:77182136 (GRCh38)
Gene constraint: LOEUF 0.995 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73 · 1 PDB
Residue 1030: the myth4 1 domain

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

Disease context

Usher syndrome type 1B — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MYO7A p.Asp1030Glu 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
MYO7A p.Glu968Asp 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-asp1030 (accessed [today's date]).

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