Is TRAP1 p.Ser477= (c.1431C>T) pathogenic?

TRAP1 p.Ser477= (c.1431C>T) is classified Likely benign in TRAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-01). Ultra-rare (popmax 0.0286%, sas).

How common is TRAP1 p.Ser477= (c.1431C>T) in the general population?

TRAP1 p.Ser477= (c.1431C>T) is ultra-rare (popmax 0.0286%, sas) (gnomAD).

TRAP1 p.Ser477=

c.1431C>T · rs780424369 · VCV2646127

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0286%, sas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -12	GERP -3.5
Overall
CADD	0.075	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0286% South Asian · 26/90,790 alleles

Filtering AF 0.02% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0172%

Overall 0.00757% 122/1,611,808 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0286%	3,492
African / African-American	0.0227%	4,406
Remaining individualsnot grpmax-eligible	0.0209%	4,794
Admixed American	0.00838%	11,933
East Asian	0.00669%	14,945
European (non-Finnish)	0.00492%	20,332

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.Ser477=
Coding: c.1431C>T
MANE Select: NM_005223 · reported on NM_016292
dbSNP: rs780424369
Type: single nucleotide variant
Location: chr16:3664412 (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-ser477 (accessed [today's date]).

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