Is TRAIP p.Ser309= (c.927C>T) pathogenic?

TRAIP p.Ser309= (c.927C>T) is classified Likely benign in TRAIP (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-11). Very rare (popmax 0.00134%, afr).

How common is TRAIP p.Ser309= (c.927C>T) in the general population?

TRAIP p.Ser309= (c.927C>T) is very rare (popmax 0.00134%, afr) (gnomAD).

TRAIP p.Ser309=

c.927C>T · VCV3649607

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.9	GERP -2, phastCons 1
Overall
CADD	8.861	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00134% African / African-American · 1/74,436 alleles

Overall 0.000657% 1/152,164 alleles · very rare

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: TRAIP
Protein: p.Ser309=
Coding: c.927C>T
MANE Select: NM_005879
Type: single nucleotide variant
Location: chr3:49832026 (GRCh38)
Gene constraint: LOEUF 0.739 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.24 · 1 PDB
Residue 309: the 'interaction with cyld' region

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

Similar variants

TRAIP p.Arg436Cys Uncertain significance ★★ ⚠ same type
TRAIP p.Arg436His Uncertain significance ★★ ⚠ same type
TRAIP p.Asp244His Uncertain significance ★★ ⚠ same type
TRAIP p.Asp431Gly Uncertain significance ★★ ⚠ same type
TRAIP p.Gln36Arg Uncertain significance ★★ ⚠ same type
TRAIP p.Glu209Lys Uncertain significance ★★ ⚠ same type
TRAIP p.Gly421Ser Uncertain significance ★★ ⚠ same type
TRAIP p.Ile104Met 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/traip-p-ser309 (accessed [today's date]).

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