Is TRAP1 p.Ser511= (c.1533A>G) pathogenic?

TRAP1 p.Ser511= (c.1533A>G) is classified Likely benign in TRAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-26). Ultra-rare (popmax 0.011%, sas).

How common is TRAP1 p.Ser511= (c.1533A>G) in the general population?

TRAP1 p.Ser511= (c.1533A>G) is ultra-rare (popmax 0.011%, sas) (gnomAD).

TRAP1 p.Ser511=

c.1533A>G · VCV4696233

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.011%, sas)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

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 -9.4	GERP -3.5
Overall
CADD	0.444	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.011% South Asian · 10/90,598 alleles

Filtering AF 0.00597% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00455%

Overall 0.00124% 20/1,609,876 alleles · ultra-rare exomes 15/1,458,046 · genomes 5/151,830 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.011%	9,060
East Asian	0.00894%	11,191
Remaining individualsnot grpmax-eligible	0.00642%	15,572
African / African-American	0.00134%	74,610
European (non-Finnish)	8.48e-05%	1,178,605

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.Ser511=
Coding: c.1533A>G
MANE Select: NM_016292
Type: single nucleotide variant
Location: chr16:3664310 (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-ser511 (accessed [today's date]).

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