Is DRAP1 p.Lys4Gln (c.10A>C) pathogenic?

DRAP1 p.Lys4Gln (c.10A>C) is classified Uncertain significance in DRAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-28). AlphaMissense: likely pathogenic (0.938); Very rare (popmax 8.74e-05%, nfe).

How common is DRAP1 p.Lys4Gln (c.10A>C) in the general population?

DRAP1 p.Lys4Gln (c.10A>C) is very rare (popmax 8.74e-05%, nfe) (gnomAD).

What do computational predictors say about DRAP1 p.Lys4Gln (c.10A>C)?

AlphaMissense predicts likely pathogenic (score 0.938) — an in-silico prediction, not a clinical call.

DRAP1 p.Lys4Gln

c.10A>C · VCV3505161

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.938 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.74e-05%, nfe)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.938	likely pathogenic
REVEL	0.069	moderately benign-leaning
SaProt	LLR -11.02	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 10	GERP 0.93, phastCons 1
Regional constraint	o/e 0.50	unconstrained · MANE · 326 bp · p 0.0012 · regional, not allelic
Overall
CADD	25.0	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

Grpmax group 8.74e-05% European (non-Finnish) · 1/1,143,622 alleles

Overall 7.2e-05% 1/1,389,850 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: DRAP1
Protein: p.Lys4Gln
Coding: c.10A>C
MANE Select: NM_006442
Type: single nucleotide variant
Location: chr11:65919511 (GRCh38)
Gene constraint: LOEUF 0.738 · pLI 0.18 (gnomAD)
Structure: AlphaFold pLDDT 73.87 · 1 PDB

Full DRAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DRAP1 p.Arg109Cys Uncertain significance ★ ⚠ same type
DRAP1 p.Arg112Trp Uncertain significance ★ ⚠ same type
DRAP1 p.Asn100Asp Uncertain significance ★ ⚠ same type
DRAP1 p.Asp105His Uncertain significance ★ ⚠ same type
DRAP1 p.Asp130Glu Uncertain significance ★ ⚠ same type
DRAP1 p.Asp196Asn Uncertain significance ★ ⚠ same type
DRAP1 p.Gln55His Uncertain significance ★ ⚠ same type
DRAP1 p.Glu198Asp 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/drap1-p-lys4gln (accessed [today's date]).

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