Is TAP1 p.Pro53= (c.159A>G) pathogenic?

TAP1 p.Pro53= (c.159A>G) is classified Likely benign in TAP1 (ClinVar, Single submitter, 2 submitters; last evaluated 2025-12-28). Rare (popmax 0.115%, afr); Associated with MHC class I deficiency.

What condition is associated with TAP1 p.Pro53= (c.159A>G)?

TAP1 p.Pro53= (c.159A>G) is associated with MHC class I deficiency (ClinVar).

How common is TAP1 p.Pro53= (c.159A>G) in the general population?

TAP1 p.Pro53= (c.159A>G) is rare (popmax 0.115%, afr) (gnomAD).

TAP1 p.Pro53=

Q: How is Immunodeficiency by defective expression of MHC class I inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.159A>G · rs144037908 · VCV534735

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.115%, afr)

Conditions

MHC class I deficiency

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 -0.4	GERP 0.15
Overall
CADD	12.82	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.115% African / African-American · 86/74,952 alleles

Filtering AF 0.0951% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0879%

Overall 0.00987% 159/1,610,168 alleles · rare exomes 102/1,457,884 · genomes 57/152,284 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.115%	872
Admixed American	0.0551%	1,816
Middle Eastern	0.0331%	3,025
Remaining individualsnot grpmax-eligible	0.0225%	4,449
European (non-Finnish)	0.00204%	49,087

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: TAP1
Protein: p.Pro53=
Coding: c.159A>G
MANE Select: NM_000593
dbSNP: rs144037908
Type: single nucleotide variant
Location: chr6:32853478 (GRCh38)
Gene constraint: LOEUF 0.876 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.03 · 22 PDB

Full TAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

MHC class I deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Immunodeficiency by defective expression of MHC class I (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood

Similar variants

TAP1 p.Arg378Ter Pathogenic ★★ same condition
TAP1 p.Gln522Ter Pathogenic/Likely pathogenic ★★ same condition
TAP1 c.-20G>C Uncertain significance ★★ ⚠ same condition
TAP1 c.-59C>T Uncertain significance ★★ ⚠ same condition
TAP1 p.Ala101Val Uncertain significance ★★ ⚠ same condition
TAP1 p.Ala2Thr Uncertain significance ★★ ⚠ same condition
TAP1 p.Ala59Thr Uncertain significance ★★ ⚠ same condition
TAP1 p.Arg129Lys 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/tap1-p-pro53 (accessed [today's date]).

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