Is CAMSAP2 p.Phe367Tyr (c.1100T>A) pathogenic?

CAMSAP2 p.Phe367Tyr (c.1100T>A) is classified Uncertain significance in CAMSAP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-24). AlphaMissense: likely benign (0.0885); Very rare (popmax 0.000173%, nfe).

How common is CAMSAP2 p.Phe367Tyr (c.1100T>A) in the general population?

CAMSAP2 p.Phe367Tyr (c.1100T>A) is very rare (popmax 0.000173%, nfe) (gnomAD).

What do computational predictors say about CAMSAP2 p.Phe367Tyr (c.1100T>A)?

AlphaMissense predicts likely benign (score 0.0885) — an in-silico prediction, not a clinical call.

CAMSAP2 p.Phe367Tyr

c.1100T>A · VCV3484547

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0885 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000173%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0885	likely benign
REVEL	0.096	moderately benign-leaning
SaProt	LLR -6.29	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 1.6	GERP 0.57, phastCons 0.013
Regional constraint	o/e 0.97	unconstrained · MANE · 6,866 bp · p 0.48 · regional, not allelic
Overall
CADD	19.1	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 F378Y vs ClinVar F367Y) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000173% European (non-Finnish) · 2/1,156,686 alleles

Filtering AF 2.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000141% 2/1,420,944 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.Phe367Tyr
Coding: c.1100T>A
MANE Select: NM_203459
Type: single nucleotide variant
Location: chr1:200844860 (GRCh38)
Gene constraint: LOEUF 0.196 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 57.60

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-phe367tyr (accessed [today's date]).

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