Is TAP1 p.Arg37Pro (c.110G>C) pathogenic?

TAP1 p.Arg37Pro (c.110G>C) is classified Uncertain significance in TAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-31). AlphaMissense: likely benign (0.0784); Very rare (popmax 8.65e-05%, nfe); Associated with Inborn genetic diseases.

What condition is associated with TAP1 p.Arg37Pro (c.110G>C)?

TAP1 p.Arg37Pro (c.110G>C) is associated with Inborn genetic diseases (ClinVar).

How common is TAP1 p.Arg37Pro (c.110G>C) in the general population?

TAP1 p.Arg37Pro (c.110G>C) is very rare (popmax 8.65e-05%, nfe) (gnomAD).

What do computational predictors say about TAP1 p.Arg37Pro (c.110G>C)?

AlphaMissense predicts likely benign (score 0.0784) — an in-silico prediction, not a clinical call.

TAP1 p.Arg37Pro

c.110G>C · rs1314187833 · VCV3173810

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0784 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.65e-05%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, REVEL · SaProt no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0784	likely benign
REVEL	0.212	benign-leaning
SaProt	—	withheld · numbering disagrees past residue 30 · why
⇒ AlphaMissense and REVEL both call this tolerated; SaProt makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.6	GERP -2.6
Overall
CADD	0.147	PHRED · no single calibrated threshold — expert panels disagree

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

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.65e-05% European (non-Finnish) · 1/1,155,766 alleles

Overall 6.42e-05% 1/1,557,596 alleles · very rare exomes 1/1,405,290 · genomes 0/152,306 · joint denominator

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.Arg37Pro
Coding: c.110G>C
MANE Select: NM_000593
dbSNP: rs1314187833
Type: single nucleotide variant
Location: chr6:32853707 (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

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

Similar variants

TAP1 p.Arg37Trp Uncertain significance ★ ⚠ same residue
TAP1 c.-20G>C Uncertain significance ★★ ⚠ same condition
TAP1 c.-59C>T 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
TAP1 p.Arg575Cys Uncertain significance ★★ ⚠ same condition
TAP1 p.Arg659Trp 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-arg37pro (accessed [today's date]).

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