Is MYO7A p.Thr1571= (c.4713G>A) pathogenic?

MYO7A p.Thr1571= (c.4713G>A) is classified Likely benign in MYO7A (ClinVar, Single submitter, 2 submitters; last evaluated 2023-11-08). Ultra-rare (popmax 0.0165%, sas); Associated with Usher syndrome type 1B.

What condition is associated with MYO7A p.Thr1571= (c.4713G>A)?

MYO7A p.Thr1571= (c.4713G>A) is associated with Usher syndrome type 1B (ClinVar).

How common is MYO7A p.Thr1571= (c.4713G>A) in the general population?

MYO7A p.Thr1571= (c.4713G>A) is ultra-rare (popmax 0.0165%, sas) (gnomAD).

MYO7A p.Thr1571=

c.4713G>A · rs568414079 · VCV1133851

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, 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	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -6.1	GERP -2.8
Overall
CADD	1.27	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0165% South Asian · 15/90,986 alleles

Filtering AF 0.0101% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00812%

Overall 0.00149% 24/1,613,316 alleles · ultra-rare exomes 21/1,461,032 · genomes 3/152,284 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0165%	6,066
East Asian	0.00223%	44,868
Admixed American	0.00167%	59,926
Remaining individualsnot grpmax-eligible	0.0016%	62,470
European (non-Finnish)	0.000509%	196,631

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.Thr1571=
Coding: c.4713G>A
MANE Select: NM_000260
dbSNP: rs568414079
Type: single nucleotide variant
Location: chr11:77199679 (GRCh38)
Gene constraint: LOEUF 0.995 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73 · 1 PDB
Residue 1571: a modified residue (phosphothreonine); the ferm 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.Thr1571Ser Uncertain significance ★★ ⚠ same residue
MYO7A p.Thr1571Met 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

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-thr1571 (accessed [today's date]).

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