Is CAMSAP2 p.Met1237Thr (c.3710T>C) pathogenic?

CAMSAP2 p.Met1237Thr (c.3710T>C) is classified Uncertain significance in CAMSAP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-26). AlphaMissense: likely pathogenic (0.6867); Very rare (popmax 0.00133%, afr).

How common is CAMSAP2 p.Met1237Thr (c.3710T>C) in the general population?

CAMSAP2 p.Met1237Thr (c.3710T>C) is very rare (popmax 0.00133%, afr) (gnomAD).

What do computational predictors say about CAMSAP2 p.Met1237Thr (c.3710T>C)?

AlphaMissense predicts likely pathogenic (score 0.6867) — an in-silico prediction, not a clinical call.

CAMSAP2 p.Met1237Thr

c.3710T>C · VCV4218565

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6867 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.6867	likely pathogenic
REVEL	0.315	indeterminate
SaProt	LLR -7.10	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.8	GERP 0.67, phastCons 1
Regional constraint	o/e 0.78	unconstrained · MANE · 7,150 bp · p 5.7e-09 · regional, not allelic
Overall
CADD	24.4	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM M1248T vs ClinVar M1237T) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00133% African / African-American · 1/75,026 alleles

Overall 6.84e-05% 1/1,461,602 alleles · very rare

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.Met1237Thr
Coding: c.3710T>C
MANE Select: NM_203459
Type: single nucleotide variant
Location: chr1:200853382 (GRCh38)
Gene constraint: LOEUF 0.196 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 57.60
Residue 1237: the 'disordered' region

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

Similar variants

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
CAMSAP2 p.Ala37Ser 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-met1237thr (accessed [today's date]).

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