Is WHRN p.Gln643= (c.1929G>A) pathogenic?

WHRN p.Gln643= (c.1929G>A) is classified Uncertain significance in WHRN (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). No allele count reported in gnomAD v4.1 (AN 1,613,870); Associated with autosomal recessive nonsyndromic hearing loss 31.

What condition is associated with WHRN p.Gln643= (c.1929G>A)?

WHRN p.Gln643= (c.1929G>A) is associated with autosomal recessive nonsyndromic hearing loss 31, Usher syndrome type 2D (ClinVar).

How common is WHRN p.Gln643= (c.1929G>A) in the general population?

WHRN p.Gln643= (c.1929G>A) is no allele count reported in gnomAD v4.1 (AN 1,613,870) (gnomAD).

WHRN p.Gln643=

c.1929G>A · rs1835054839 · VCV912538

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,870)

Conditions

autosomal recessive nonsyndromic hearing loss 31

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 1.1	GERP -0.23, phastCons 1
Overall
CADD	4.342	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,613,870). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: WHRN
Protein: p.Gln643=
Coding: c.1929G>A
MANE Select: NM_015404
dbSNP: rs1835054839
Type: single nucleotide variant
Location: chr9:114406662 (GRCh38)
Gene constraint: LOEUF 0.808 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 59.39 · 5 PDB
Residue 643: the 'disordered' region

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

Disease context

autosomal recessive nonsyndromic hearing loss 31 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Usher syndrome type 2D

Similar variants

WHRN p.Gln643Leu Uncertain significance ★ ⚠ same residue
WHRN c.1417-1G>A Pathogenic/Likely pathogenic ★★ same condition
WHRN p.Arg778Ter Pathogenic ★★ same condition
WHRN c.*156G>A Uncertain significance ★★ same condition
WHRN p.Ala631Val Uncertain significance ★★ ⚠ same condition
WHRN p.Ala885Thr Uncertain significance ★★ ⚠ same condition
WHRN p.Arg366His Uncertain significance ★★ ⚠ same condition
WHRN p.Arg490His Uncertain significance ★★ ⚠ 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/whrn-p-gln643 (accessed [today's date]).

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