Is CAMTA2 p.Arg970Pro (c.2909G>C) pathogenic?

CAMTA2 p.Arg970Pro (c.2909G>C) is classified Uncertain significance in CAMTA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-07). AlphaMissense: likely benign (0.1747); Very rare (popmax 0.00267%, afr).

How common is CAMTA2 p.Arg970Pro (c.2909G>C) in the general population?

CAMTA2 p.Arg970Pro (c.2909G>C) is very rare (popmax 0.00267%, afr) (gnomAD).

What do computational predictors say about CAMTA2 p.Arg970Pro (c.2909G>C)?

AlphaMissense predicts likely benign (score 0.1747) — an in-silico prediction, not a clinical call.

CAMTA2 p.Arg970Pro

c.2909G>C · VCV3827117

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1747 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00267%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1747	likely benign
REVEL	0.148	moderately benign-leaning
SaProt	LLR -5.20	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 1.1	GERP -0.67, phastCons 0.94
Regional constraint	o/e 0.96	unconstrained · MANE · 12 kb · p 0.13 · regional, not allelic
Overall
CADD	17.17	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 0.00267% African / African-American · 2/74,900 alleles

Filtering AF 0.000615% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000474%

Overall 0.000929% 15/1,614,026 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00267%	37,450
European (non-Finnish)	0.0011%	90,771

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.Arg970Pro
Coding: c.2909G>C
MANE Select: NM_015099
Type: single nucleotide variant
Location: chr17:4970436 (GRCh38)
Gene constraint: LOEUF 0.512 · pLI 0.28 (gnomAD)
Structure: AlphaFold pLDDT 60.82

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

Similar variants

CAMTA2 p.Arg970Gln Uncertain significance ★ ⚠ same residue
CAMTA2 p.Arg970Trp Uncertain significance ★ ⚠ same residue
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

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-arg970pro (accessed [today's date]).

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