Is DRAP1 p.Thr174Pro (c.520A>C) pathogenic?

DRAP1 p.Thr174Pro (c.520A>C) is classified Uncertain significance in DRAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-02). AlphaMissense: likely benign (0.056); Absent from gnomAD v4.1.

How common is DRAP1 p.Thr174Pro (c.520A>C) in the general population?

DRAP1 p.Thr174Pro (c.520A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DRAP1 p.Thr174Pro (c.520A>C)?

AlphaMissense predicts likely benign (score 0.056) — an in-silico prediction, not a clinical call.

DRAP1 p.Thr174Pro

c.520A>C · rs1854547882 · VCV3085711

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.056 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.056	likely benign
REVEL	0.078	moderately benign-leaning
SaProt	LLR -2.32	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 1.5	GERP 0.24, phastCons 0.17
Regional constraint	o/e 1.04	unconstrained · MANE · 1,603 bp · p 0.54 · regional, not allelic
Overall
CADD	13.27	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: DRAP1
Protein: p.Thr174Pro
Coding: c.520A>C
MANE Select: NM_006442
dbSNP: rs1854547882
Type: single nucleotide variant
Location: chr11:65921337 (GRCh38)
Gene constraint: LOEUF 0.738 · pLI 0.18 (gnomAD)
Structure: AlphaFold pLDDT 73.87 · 1 PDB
Residue 174: the 'disordered' region

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-thr174pro (accessed [today's date]).

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