Is CAAP1 p.Gly56Ala (c.167G>C) pathogenic?

CAAP1 p.Gly56Ala (c.167G>C) is classified Uncertain significance in CAAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-21). AlphaMissense: likely benign (0.1442); Ultra-rare (popmax 0.024%, nfe).

How common is CAAP1 p.Gly56Ala (c.167G>C) in the general population?

CAAP1 p.Gly56Ala (c.167G>C) is ultra-rare (popmax 0.024%, nfe) (gnomAD).

What do computational predictors say about CAAP1 p.Gly56Ala (c.167G>C)?

AlphaMissense predicts likely benign (score 0.1442) — an in-silico prediction, not a clinical call.

CAAP1 p.Gly56Ala

c.167G>C · rs758201016 · VCV2382867

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1442 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.024%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1442	likely benign
REVEL	0.155	moderately benign-leaning
SaProt	LLR -8.88	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 3.1	GERP 0.59, phastCons 1
Regional constraint	o/e 1.26	unconstrained · MANE · 50 kb · p 1.7e-07 · regional, not allelic
Overall
CADD	21.6	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 0.024% European (non-Finnish) · 279/1,163,894 alleles

Filtering AF 0.0216% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0208%

Overall 0.019% 300/1,580,998 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.024%	4,172
Finnishnot grpmax-eligible	0.0216%	4,626
Remaining individualsnot grpmax-eligible	0.0098%	10,209
African / African-American	0.00269%	37,140

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: CAAP1
Protein: p.Gly56Ala
Coding: c.167G>C
MANE Select: NM_024828
dbSNP: rs758201016
Type: single nucleotide variant
Location: chr9:26892549 (GRCh38)
Gene constraint: LOEUF 1.136 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.18

Full CAAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CAAP1 p.Ala209Val Uncertain significance ★ ⚠ same type
CAAP1 p.Ala22Glu Uncertain significance ★ ⚠ same type
CAAP1 p.Ala261Gly Uncertain significance ★ ⚠ same type
CAAP1 p.Ala288Gly Uncertain significance ★ ⚠ same type
CAAP1 p.Ala322Ser Uncertain significance ★ ⚠ same type
CAAP1 p.Ala347Pro Uncertain significance ★ ⚠ same type
CAAP1 p.Ala354Pro Uncertain significance ★ ⚠ same type
CAAP1 p.Arg12Gly 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/caap1-p-gly56ala (accessed [today's date]).

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