Is CAMSAP3 p.Ala196Pro (c.586G>C) pathogenic?

CAMSAP3 p.Ala196Pro (c.586G>C) is classified Uncertain significance in CAMSAP3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-29). AlphaMissense: likely benign (0.0906); Absent from gnomAD v4.1.

How common is CAMSAP3 p.Ala196Pro (c.586G>C) in the general population?

CAMSAP3 p.Ala196Pro (c.586G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CAMSAP3 p.Ala196Pro (c.586G>C)?

AlphaMissense predicts likely benign (score 0.0906) — an in-silico prediction, not a clinical call.

CAMSAP3 p.Ala196Pro

c.586G>C · VCV4218585

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0906 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0906	likely benign
REVEL	0.052	moderately benign-leaning
SaProt	LLR -6.12	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 1.8	phastCons 0.81
Regional constraint	o/e 1.19	unconstrained · MANE · 1,820 bp · p 0.067 · regional, not allelic
Overall
CADD	15.43	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: CAMSAP3
Protein: p.Ala196Pro
Coding: c.586G>C
MANE Select: NM_020902
Type: single nucleotide variant
Location: chr19:7606536 (GRCh38)
Gene constraint: LOEUF 0.51 · pLI 0.88 (gnomAD)
Structure: AlphaFold pLDDT 60.70
Residue 196: the 'disordered' region

Full CAMSAP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CAMSAP3 p.Ala239= Benign ★★ same type
CAMSAP3 p.Arg931Gln Benign ★★ same type
CAMSAP3 p.Pro381= Benign ★★ same type
CAMSAP3 p.Tyr294= Benign ★★ same type
CAMSAP3 c.622-299A>G Uncertain significance ★ same type
CAMSAP3 p.Ala1002Val Uncertain significance ★ ⚠ same type
CAMSAP3 p.Ala1098Val Uncertain significance ★ ⚠ same type
CAMSAP3 p.Ala1118Thr 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/camsap3-p-ala196pro (accessed [today's date]).

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