Is MYO7A p.Thr1796= (c.5388C>T) pathogenic?

MYO7A p.Thr1796= (c.5388C>T) is classified Likely benign in MYO7A (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-03-25). Ultra-rare (popmax 0.0409%, eas); Associated with Usher syndrome type 1B.

What condition is associated with MYO7A p.Thr1796= (c.5388C>T)?

MYO7A p.Thr1796= (c.5388C>T) is associated with Usher syndrome type 1B (ClinVar).

How common is MYO7A p.Thr1796= (c.5388C>T) in the general population?

MYO7A p.Thr1796= (c.5388C>T) is ultra-rare (popmax 0.0409%, eas) (gnomAD).

MYO7A p.Thr1796=

c.5388C>T · rs372062718 · VCV669179

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0409%, eas)

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 -16	GERP -3.2
Overall
CADD	0.508	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0409% East Asian · 18/43,974 alleles

Filtering AF 0.0264% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0218%

Overall 0.00463% 74/1,598,962 alleles · ultra-rare exomes 68/1,446,632 · genomes 6/152,330 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0409%	2,443
African / African-American	0.0067%	14,921
European (non-Finnish)	0.00401%	24,959
Remaining individualsnot grpmax-eligible	0.00323%	31,000
South Asian	0.00228%	43,955

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.Thr1796=
Coding: c.5388C>T
MANE Select: NM_000260
dbSNP: rs372062718
Type: single nucleotide variant
Location: chr11:77204137 (GRCh38)
Gene constraint: LOEUF 0.995 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73 · 1 PDB
Residue 1796: the myth4 2 domain; an α-helix

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-thr1796 (accessed [today's date]).

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