Is CAMSAP2 p.Pro958Ser (c.2872C>T) pathogenic?

CAMSAP2 p.Pro958Ser (c.2872C>T) is classified Uncertain significance in CAMSAP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-02). AlphaMissense: likely benign (0.0673); Ultra-rare (popmax 0.0164%, mid).

How common is CAMSAP2 p.Pro958Ser (c.2872C>T) in the general population?

CAMSAP2 p.Pro958Ser (c.2872C>T) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

What do computational predictors say about CAMSAP2 p.Pro958Ser (c.2872C>T)?

AlphaMissense predicts likely benign (score 0.0673) — an in-silico prediction, not a clinical call.

CAMSAP2 p.Pro958Ser

c.2872C>T · VCV3827075

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0673 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0673	likely benign
REVEL	0.053	moderately benign-leaning
SaProt	LLR -5.36	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 0.24	GERP 0.15
Regional constraint	o/e 0.78	unconstrained · MANE · 7,150 bp · p 5.7e-09 · regional, not allelic
Overall
CADD	19.01	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.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM P969S vs ClinVar P958S) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0164% Middle Eastern · 1/6,084 alleles

Filtering AF 0.000183% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00012%

Overall 0.000434% 7/1,614,062 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,084
European (non-Finnish)	0.000508%	196,671

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: CAMSAP2
Protein: p.Pro958Ser
Coding: c.2872C>T
MANE Select: NM_203459
Type: single nucleotide variant
Location: chr1:200849641 (GRCh38)
Gene constraint: LOEUF 0.196 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 57.60
Residue 958: a UniProt-annotated variant site (in); the 'mbd region' region; the 'disordered' region

Full CAMSAP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CAMSAP2 p.Pro958Leu Uncertain significance ★ ⚠ same residue
CAMSAP2 p.Ser748Cys Uncertain significance ★★ ⚠ same type
CAMSAP2 p.Pro1028Arg Benign ★★ same type
CAMSAP2 p.Ala1331Val Uncertain significance ★ ⚠ same type
CAMSAP2 p.Ala1450Gly Uncertain significance ★ ⚠ same type
CAMSAP2 p.Ala146Thr Uncertain significance ★ ⚠ same type
CAMSAP2 p.Ala356Val Uncertain significance ★ ⚠ same type
CAMSAP2 p.Ala374Ser 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/camsap2-p-pro958ser (accessed [today's date]).

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