Is DLX5 p.Val111Ile (c.331G>A) pathogenic?

DLX5 p.Val111Ile (c.331G>A) is classified Uncertain significance in DLX5 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-04). AlphaMissense: likely benign (0.0755); Absent from gnomAD v4.1.

How common is DLX5 p.Val111Ile (c.331G>A) in the general population?

DLX5 p.Val111Ile (c.331G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DLX5 p.Val111Ile (c.331G>A)?

AlphaMissense predicts likely benign (score 0.0755) — an in-silico prediction, not a clinical call.

DLX5 p.Val111Ile

c.331G>A · rs921422739 · VCV2036668

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0755 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0755	likely benign
REVEL	0.223	benign-leaning
SaProt	LLR -7.34	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.6	GERP 1.2, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 2,376 bp · p 0.21 · regional, not allelic
Overall
CADD	19.63	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: DLX5
Protein: p.Val111Ile
Coding: c.331G>A
MANE Select: NM_005221
dbSNP: rs921422739
Type: single nucleotide variant
Location: chr7:97024293 (GRCh38)
Gene constraint: LOEUF 0.498 · pLI 0.98 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 61.56 · 2 PDB

Full DLX5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DLX5 p.Asp44Tyr Uncertain significance ★★ ⚠ same type
DLX5 p.Asp46Glu Uncertain significance ★★ ⚠ same type
DLX5 p.His238Asn Uncertain significance ★★ ⚠ same type
DLX5 p.His279Tyr Uncertain significance ★★ ⚠ same type
DLX5 p.Pro30Leu Uncertain significance ★★ ⚠ same type
DLX5 p.Ser229Pro Uncertain significance ★★ ⚠ same type
DLX5 p.Tyr108Cys Uncertain significance ★★ ⚠ same type
DLX5 c.540+227C>T Likely benign ★★ 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/dlx5-p-val111ile (accessed [today's date]).

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