Is CAMTA2 p.Ser520Arg (c.1560C>G) pathogenic?

CAMTA2 p.Ser520Arg (c.1560C>G) is classified Uncertain significance in CAMTA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-30). AlphaMissense: likely benign (0.1947); Absent from gnomAD v4.1.

How common is CAMTA2 p.Ser520Arg (c.1560C>G) in the general population?

CAMTA2 p.Ser520Arg (c.1560C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CAMTA2 p.Ser520Arg (c.1560C>G)?

AlphaMissense predicts likely benign (score 0.1947) — an in-silico prediction, not a clinical call.

CAMTA2 p.Ser520Arg

c.1560C>G · VCV3263100

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1947 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1947	likely benign
REVEL	0.066	moderately benign-leaning
SaProt	LLR -7.76	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 -0.034	GERP 0.45
Regional constraint	o/e 0.96	unconstrained · MANE · 12 kb · p 0.13 · regional, not allelic
Overall
CADD	12.32	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CAMTA2
Protein: p.Ser520Arg
Coding: c.1560C>G
MANE Select: NM_015099
Type: single nucleotide variant
Location: chr17:4979762 (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.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-ser520arg (accessed [today's date]).

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