Is CPTP p.Arg90Gln (c.269G>A) pathogenic?

CPTP p.Arg90Gln (c.269G>A) is classified Likely benign in CPTP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-08). AlphaMissense: likely benign (0.0646); Ultra-rare (popmax 0.0246%, eas).

How common is CPTP p.Arg90Gln (c.269G>A) in the general population?

CPTP p.Arg90Gln (c.269G>A) is ultra-rare (popmax 0.0246%, eas) (gnomAD).

What do computational predictors say about CPTP p.Arg90Gln (c.269G>A)?

AlphaMissense predicts likely benign (score 0.0646) — an in-silico prediction, not a clinical call.

CPTP p.Arg90Gln

c.269G>A · rs749538987 · VCV3076943

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0646 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0246%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0646	likely benign
REVEL	0.118	moderately benign-leaning
SaProt	LLR -6.06	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.5	GERP -1.7, phastCons 1
Regional constraint	o/e 1.09	unconstrained · MANE · 849 bp · p 0.1 · regional, not allelic
Overall
CADD	13.11	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0246% East Asian · 11/44,758 alleles

Filtering AF 0.0137% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0106%

Overall 0.00294% 47/1,597,214 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0246%	4,069
African / African-American	0.0107%	9,355
Remaining individualsnot grpmax-eligible	0.00965%	10,366
South Asian	0.00441%	22,688
Finnishnot grpmax-eligible	0.00199%	50,330
Admixed American	0.00168%	59,680
European (non-Finnish)	0.00136%	73,638

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: CPTP
Protein: p.Arg90Gln
Coding: c.269G>A
MANE Select: NM_001029885
dbSNP: rs749538987
Type: single nucleotide variant
Location: chr1:1327387 (GRCh38)
Gene constraint: LOEUF 1.748 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.93 · 6 PDB

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

Similar variants

CPTP p.Ala132Thr Uncertain significance ★ ⚠ same type
CPTP p.Arg106Gln Uncertain significance ★ ⚠ same type
CPTP p.Arg106Gly Uncertain significance ★ same type
CPTP p.Arg106Trp Uncertain significance ★ ⚠ same type
CPTP p.Arg110Cys Uncertain significance ★ ⚠ same type
CPTP p.Arg110His Uncertain significance ★ ⚠ same type
CPTP p.Arg126Cys Uncertain significance ★ ⚠ same type
CPTP p.Arg133Cys 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/cptp-p-arg90gln (accessed [today's date]).

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