Is HYOU1 p.Lys894= (c.2682G>A) pathogenic?

HYOU1 p.Lys894= (c.2682G>A) is classified Likely benign in HYOU1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-16). Absent from gnomAD v4.1.

How common is HYOU1 p.Lys894= (c.2682G>A) in the general population?

HYOU1 p.Lys894= (c.2682G>A) is absent from gnomAD v4.1 (gnomAD).

HYOU1 p.Lys894=

c.2682G>A · rs1944100735 · VCV2026035

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 2.2	GERP 1.9, phastCons 1
Overall
CADD	9.186	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: HYOU1
Protein: p.Lys894=
Coding: c.2682G>A
MANE Select: NM_006389
dbSNP: rs1944100735
Type: single nucleotide variant
Location: chr11:119046716 (GRCh38)
Gene constraint: LOEUF 0.41 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 81.96

Full HYOU1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

HYOU1 c.2253+6T>G Uncertain significance ★★ same type
HYOU1 p.Ala191Ser Uncertain significance ★★ ⚠ same type
HYOU1 p.Ala28Gly Uncertain significance ★★ ⚠ same type
HYOU1 p.Ala324Thr Uncertain significance ★★ ⚠ same type
HYOU1 p.Ala324Val Uncertain significance ★★ ⚠ same type
HYOU1 p.Ala425Val Uncertain significance ★★ ⚠ same type
HYOU1 p.Ala568Thr Uncertain significance ★★ ⚠ same type
HYOU1 p.Ala777Thr Uncertain significance ★★ ⚠ same type

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/hyou1-p-lys894 (accessed [today's date]).

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