Is TRAP1 p.Arg602Gln (c.1805G>A) pathogenic?

TRAP1 p.Arg602Gln (c.1805G>A) is classified Conflicting classifications of pathogenicity in TRAP1 (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2025-12-16). AlphaMissense: ambiguous (0.4512); Rare (popmax 0.482%, afr).

How common is TRAP1 p.Arg602Gln (c.1805G>A) in the general population?

TRAP1 p.Arg602Gln (c.1805G>A) is rare (popmax 0.482%, afr) (gnomAD).

What do computational predictors say about TRAP1 p.Arg602Gln (c.1805G>A)?

AlphaMissense predicts ambiguous (score 0.4512) — an in-silico prediction, not a clinical call.

TRAP1 p.Arg602Gln

c.1805G>A · rs138615105 · VCV734841

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

AlphaMissense

ambiguous

0.4512 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.482%, afr)

Computational evidence

Protein change
AlphaMissense	0.4512	ambiguous
REVEL	0.542	indeterminate
SaProt	LLR -10.14	damaging
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 4.8	GERP 1.7, phastCons 1
Regional constraint	o/e 1.33	unconstrained · MANE · 59 kb · p 5.2e-24 · regional, not allelic
Overall
CADD	29.2	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 0.482% African / African-American · 362/75,030 alleles

Filtering AF 0.441% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.425%

Overall 0.0336% 541/1,611,974 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.482%	207
Admixed American	0.0652%	1,535
Remaining individualsnot grpmax-eligible	0.0385%	2,601
Middle Eastern	0.0332%	3,014
European (non-Finnish)	0.00941%	10,623
South Asian	0.0033%	30,296

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: TRAP1
Protein: p.Arg602Gln
Coding: c.1805G>A
MANE Select: NM_005223 · reported on NM_016292
dbSNP: rs138615105
Type: single nucleotide variant
Location: chr16:3662122 (GRCh38)

Full TRAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/trap1-p-arg602gln (accessed [today's date]).

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