Is USH1C p.Val189= (c.567G>T) pathogenic?

USH1C p.Val189= (c.567G>T) is classified Likely benign in USH1C (ClinVar, Single submitter, 2 submitters; last evaluated 2022-09-07). Absent from gnomAD v4.1; Associated with Usher syndrome type 1C.

What condition is associated with USH1C p.Val189= (c.567G>T)?

USH1C p.Val189= (c.567G>T) is associated with Usher syndrome type 1C (ClinVar).

How common is USH1C p.Val189= (c.567G>T) in the general population?

USH1C p.Val189= (c.567G>T) is absent from gnomAD v4.1 (gnomAD).

USH1C p.Val189=

c.567G>T · rs1850696503 · VCV992083

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Usher syndrome type 1C

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 0.43	GERP -3.4, phastCons 0.99
Overall
CADD	4.888	PHRED · no single calibrated threshold — expert panels disagree

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: USH1C
Protein: p.Val189=
Coding: c.567G>T
MANE Select: NM_153676
dbSNP: rs1850696503
Type: single nucleotide variant
Location: chr11:17526765 (GRCh38)
Gene constraint: LOEUF 0.876 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 79.51 · 11 PDB
Residue 189: an α-helix

Full USH1C gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Similar variants

USH1C c.1020-2A>C Likely pathogenic ★★ same condition
USH1C c.104+1G>A Pathogenic/Likely pathogenic ★★ same condition
USH1C c.104+5G>C Likely pathogenic ★★ same condition
USH1C c.2227-1G>T Pathogenic/Likely pathogenic ★★ same condition
USH1C c.2280+2T>C Likely pathogenic ★★ same condition
USH1C c.248+1G>A Likely pathogenic ★★ same condition
USH1C c.249-1G>A Likely pathogenic ★★ same condition
USH1C c.2490+1G>A 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/ush1c-p-val189 (accessed [today's date]).

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