Is CAMTA2 p.Pro588= (c.1764C>T) pathogenic?

CAMTA2 p.Pro588= (c.1764C>T) is classified Likely benign in CAMTA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-04). Ultra-rare (popmax 0.0253%, afr).

How common is CAMTA2 p.Pro588= (c.1764C>T) in the general population?

CAMTA2 p.Pro588= (c.1764C>T) is ultra-rare (popmax 0.0253%, afr) (gnomAD).

CAMTA2 p.Pro588=

c.1764C>T · rs191877524 · VCV3136923

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0253%, afr)

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 -4.3	GERP -3.4
Overall
CADD	1.104	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0253% African / African-American · 19/75,018 alleles

Filtering AF 0.0165% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0137%

Overall 0.0018% 29/1,613,728 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0253%	3,948
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,596
Admixed American	0.00333%	30,005
Remaining individualsnot grpmax-eligible	0.0032%	31,234
Finnishnot grpmax-eligible	0.00156%	64,004
South Asian	0.0011%	91,044
European (non-Finnish)	0.000254%	393,244

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: CAMTA2
Protein: p.Pro588=
Coding: c.1764C>T
MANE Select: NM_015099
dbSNP: rs191877524
Type: single nucleotide variant
Location: chr17:4978505 (GRCh38)
Gene constraint: LOEUF 0.512 · pLI 0.28 (gnomAD)
Structure: AlphaFold pLDDT 60.82
Residue 588: the ipt/tig domain

Full CAMTA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CAMTA2 p.Ala267Pro Benign ★★ same type
CAMTA2 p.His343= Benign ★★ same type
CAMTA2 p.Pro749= Benign ★★ same type
CAMTA2 c.1765+1G>A Uncertain significance ★ same type
CAMTA2 c.1901-2A>C Uncertain significance ★ same type
CAMTA2 c.-18C>G Uncertain significance ★ same type
CAMTA2 c.-2C>A Uncertain significance ★ same type
CAMTA2 c.-32C>T 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/camta2-p-pro588 (accessed [today's date]).

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