Is TRAP1 p.Tyr486= (c.1458C>T) pathogenic?

TRAP1 p.Tyr486= (c.1458C>T) is classified Likely benign in TRAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-03). Ultra-rare (popmax 0.0491%, eas).

How common is TRAP1 p.Tyr486= (c.1458C>T) in the general population?

TRAP1 p.Tyr486= (c.1458C>T) is ultra-rare (popmax 0.0491%, eas) (gnomAD).

TRAP1 p.Tyr486=

c.1458C>T · rs555130426 · VCV1554384

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0491%, eas)

⚠ 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 -8.6	GERP -3.5
Overall
CADD	0.04	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0491% East Asian · 22/44,842 alleles

Filtering AF 0.0332% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.028%

Overall 0.00347% 56/1,612,342 alleles · ultra-rare exomes 46/1,460,040 · genomes 10/152,302 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0491%	2,038
Admixed American	0.0117%	8,537
Remaining individualsnot grpmax-eligible	0.00802%	12,474
European (non-Finnish)	0.00178%	56,163
African / African-American	0.00133%	75,018

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.Tyr486=
Coding: c.1458C>T
MANE Select: NM_016292
dbSNP: rs555130426
Type: single nucleotide variant
Location: chr16:3664385 (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-tyr486 (accessed [today's date]).

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