Is TAP2 p.Arg313Pro (c.938G>C) pathogenic?

TAP2 p.Arg313Pro (c.938G>C) is classified Uncertain significance in TAP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-04-08). AlphaMissense: likely pathogenic (0.6991); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with TAP2 p.Arg313Pro (c.938G>C)?

TAP2 p.Arg313Pro (c.938G>C) is associated with Inborn genetic diseases (ClinVar).

How common is TAP2 p.Arg313Pro (c.938G>C) in the general population?

TAP2 p.Arg313Pro (c.938G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about TAP2 p.Arg313Pro (c.938G>C)?

AlphaMissense predicts likely pathogenic (score 0.6991) — an in-silico prediction, not a clinical call.

TAP2 p.Arg313Pro

c.938G>C · rs140654840 · VCV2282786

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6991 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.6991	likely pathogenic
REVEL	0.604	indeterminate
SaProt	LLR -14.73	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.7	GERP 1.6, phastCons 1
Overall
CADD	23.7	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: TAP2
Protein: p.Arg313Pro
Coding: c.938G>C
MANE Select: NM_001290043
dbSNP: rs140654840
Type: single nucleotide variant
Location: chr6:32835161 (GRCh38)
Structure: AlphaFold pLDDT 96.96 · 1 PDB
Residue 313: the gold domain

Full TAP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TAP2 p.Arg313Cys Uncertain significance ★★ ⚠ same residue
TAP2 p.Arg313His Benign/Likely benign ★★ same residue
TAP2 p.Ala17Val Uncertain significance ★★ ⚠ same condition
TAP2 p.Ala306Val Uncertain significance ★★ ⚠ same condition
TAP2 p.Ala500Thr Uncertain significance ★★ ⚠ same condition
TAP2 p.Arg354His Uncertain significance ★★ ⚠ same condition
TAP2 p.Arg363Trp Uncertain significance ★★ ⚠ same condition
TAP2 p.Arg619Trp Uncertain significance ★★ ⚠ same condition

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/tap2-p-arg313pro (accessed [today's date]).

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