Is PTPRCAP p.Arg55His (c.164G>A) pathogenic?

PTPRCAP p.Arg55His (c.164G>A) is classified Uncertain significance in PTPRCAP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-15). AlphaMissense: likely benign (0.073); Ultra-rare (popmax 0.0163%, afr).

How common is PTPRCAP p.Arg55His (c.164G>A) in the general population?

PTPRCAP p.Arg55His (c.164G>A) is ultra-rare (popmax 0.0163%, afr) (gnomAD).

What do computational predictors say about PTPRCAP p.Arg55His (c.164G>A)?

AlphaMissense predicts likely benign (score 0.073) — an in-silico prediction, not a clinical call.

PTPRCAP p.Arg55His

c.164G>A · rs536852844 · VCV3149320

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.073 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0163%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.073	likely benign
REVEL	0.04	moderately benign-leaning
SaProt	LLR -7.48	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -2.7	GERP -3.5
Regional constraint	o/e 1.03	unconstrained · MANE · 1,883 bp · p 0.61 · regional, not allelic
Overall
CADD	16.82	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 and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0163% African / African-American · 12/73,570 alleles

Filtering AF 0.0132% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0125%

Overall 0.0122% 189/1,553,638 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0163%	6,131
European (non-Finnish)	0.015%	6,651
Remaining individualsnot grpmax-eligible	0.00332%	30,162
South Asian	0.00235%	42,466

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: PTPRCAP
Protein: p.Arg55His
Coding: c.164G>A
MANE Select: NM_005608
dbSNP: rs536852844
Type: single nucleotide variant
Location: chr11:67436190 (GRCh38)

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

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/ptprcap-p-arg55his (accessed [today's date]).

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