Is MYO7A p.Asp1132= (c.3396C>T) pathogenic?

MYO7A p.Asp1132= (c.3396C>T) is classified Likely benign in MYO7A (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-03-13). Ultra-rare (popmax 0.0162%, afr); Associated with Usher syndrome type 1B.

What condition is associated with MYO7A p.Asp1132= (c.3396C>T)?

MYO7A p.Asp1132= (c.3396C>T) is associated with Usher syndrome type 1B (ClinVar).

How common is MYO7A p.Asp1132= (c.3396C>T) in the general population?

MYO7A p.Asp1132= (c.3396C>T) is ultra-rare (popmax 0.0162%, afr) (gnomAD).

MYO7A p.Asp1132=

c.3396C>T · rs543234546 · VCV751049

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0162%, afr)

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 -2.6
Overall
CADD	0.313	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0162% African / African-American · 12/74,002 alleles

Filtering AF 0.00932% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0073%

Overall 0.00153% 24/1,568,796 alleles · ultra-rare exomes 19/1,416,468 · genomes 5/152,328 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0162%	6,167
East Asian	0.0047%	21,263
South Asian	0.00468%	21,356
Admixed American	0.00189%	53,030
European (non-Finnish)	0.000432%	231,287

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.Asp1132=
Coding: c.3396C>T
MANE Select: NM_000260
dbSNP: rs543234546
Type: single nucleotide variant
Location: chr11:77184608 (GRCh38)
Gene constraint: LOEUF 0.995 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73 · 1 PDB
Residue 1132: 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.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
MYO7A p.Gly2187Asp 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-asp1132 (accessed [today's date]).

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