Is TAPBP p.Phe320= (c.960C>T) pathogenic?

TAPBP p.Phe320= (c.960C>T) is classified Likely benign in TAPBP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-07). Absent from gnomAD v4.1.

How common is TAPBP p.Phe320= (c.960C>T) in the general population?

TAPBP p.Phe320= (c.960C>T) is absent from gnomAD v4.1 (gnomAD).

TAPBP p.Phe320=

c.960C>T · VCV4891617

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	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.8	GERP 1.7, phastCons 1
Overall
CADD	11.39	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: TAPBP
Protein: p.Phe320=
Coding: c.960C>T
MANE Select: NM_003190
Type: single nucleotide variant
Location: chr6:33304547 (GRCh38)
Gene constraint: LOEUF 1.061 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.71 · 12 PDB
Residue 320: the ig-like c1-type domain; a β-strand

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

Similar variants

TAPBP p.Ala191Thr Uncertain significance ★★ ⚠ same type
TAPBP p.Ala220Val Uncertain significance ★★ ⚠ same type
TAPBP p.Ala305Ser Uncertain significance ★★ ⚠ same type
TAPBP p.Ala305Thr Uncertain significance ★★ ⚠ same type
TAPBP p.Ala309Glu Uncertain significance ★★ ⚠ same type
TAPBP p.Ala396Thr Uncertain significance ★★ ⚠ same type
TAPBP p.Ala433Thr Uncertain significance ★★ ⚠ same type
TAPBP p.Arg208Cys 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/tapbp-p-phe320 (accessed [today's date]).

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