Is DNHD1 p.Glu971Lys (c.2911G>A) pathogenic?

DNHD1 p.Glu971Lys (c.2911G>A) is classified Uncertain significance in DNHD1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-10-19). AlphaMissense: ambiguous (0.5058); Absent from gnomAD v4.1; Associated with DNHD1-related disorder.

What condition is associated with DNHD1 p.Glu971Lys (c.2911G>A)?

DNHD1 p.Glu971Lys (c.2911G>A) is associated with DNHD1-related disorder (ClinVar).

How common is DNHD1 p.Glu971Lys (c.2911G>A) in the general population?

DNHD1 p.Glu971Lys (c.2911G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DNHD1 p.Glu971Lys (c.2911G>A)?

AlphaMissense predicts ambiguous (score 0.5058) — an in-silico prediction, not a clinical call.

DNHD1 p.Glu971Lys

c.2911G>A · rs2494016560 · VCV3045675

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5058 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

DNHD1-related disorder

Computational evidence

Protein change
AlphaMissense	0.5058	ambiguous
REVEL	0.282	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2.2, phastCons 1
Regional constraint	o/e 0.90	unconstrained · MANE · 66 kb · p 5.3e-11 · regional, not allelic
Overall
CADD	26.5	PHRED · no single calibrated threshold — expert panels disagree

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: DNHD1
Protein: p.Glu971Lys
Coding: c.2911G>A
MANE Select: NM_144666
dbSNP: rs2494016560
Type: single nucleotide variant
Location: chr11:6534086 (GRCh38)
Gene constraint: LOEUF 0.897 · pLI <0.01 (gnomAD)

Full DNHD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DNHD1-related disorder

Similar variants

DNHD1 p.Glu4486Lys Uncertain significance ★★ ⚠ same condition
DNHD1 p.His4162Leu Uncertain significance ★★ ⚠ same condition
DNHD1 p.Arg2840Gln Uncertain significance ★ ⚠ same condition
DNHD1 p.Gln895Ter Conflicting classifications of pathogenicity ★ same condition
DNHD1 p.His3335Arg Uncertain significance ★ ⚠ same condition
DNHD1 p.Ala657Ser Uncertain significance ⚠ same condition
DNHD1 p.Met1535Val Uncertain significance ⚠ same condition
DNHD1 p.Ser920Gly 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/dnhd1-p-glu971lys (accessed [today's date]).

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