Is TRAF3IP1 p.Arg587= (c.1761C>A) pathogenic?

TRAF3IP1 p.Arg587= (c.1761C>A) is classified Likely benign in TRAF3IP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-26). Absent from gnomAD v4.1.

How common is TRAF3IP1 p.Arg587= (c.1761C>A) in the general population?

TRAF3IP1 p.Arg587= (c.1761C>A) is absent from gnomAD v4.1 (gnomAD).

TRAF3IP1 p.Arg587=

c.1761C>A · VCV4767630

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -13	GERP -2.7
Overall
CADD	0.048	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: TRAF3IP1
Protein: p.Arg587=
Coding: c.1761C>A
MANE Select: NM_015650
Type: single nucleotide variant
Location: chr2:238397530 (GRCh38)
Gene constraint: LOEUF 0.723 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.95 · 2 PDB
Residue 587: the 'disc1-interaction domain' region

Full TRAF3IP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

IFT54 p.Arg587Cys Uncertain significance ★★ ⚠ same residue
IFT54 c.1159+1G>C Likely pathogenic ★★ same type
IFT54 c.988-1G>A Likely pathogenic ★★ same type
IFT54 c.988-1G>C Likely pathogenic ★★ same type
IFT54 p.Arg565Ter Pathogenic/Likely pathogenic ★★ same type
IFT54 p.Trp572Ter Pathogenic/Likely pathogenic ★★ same type
IFT54 c.1452-5T>G Uncertain significance ★★ same type
IFT54 c.1910+3G>T 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/traf3ip1-p-arg587 (accessed [today's date]).

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