Is CAMSAP1 p.Ala1509= (c.4527C>G) pathogenic?

CAMSAP1 p.Ala1509= (c.4527C>G) is classified Likely benign in CAMSAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-03-01). Rare (popmax 0.877%, mid).

How common is CAMSAP1 p.Ala1509= (c.4527C>G) in the general population?

CAMSAP1 p.Ala1509= (c.4527C>G) is rare (popmax 0.877%, mid) (gnomAD).

CAMSAP1 p.Ala1509=

c.4527C>G · VCV3777773

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.877%, mid)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5	GERP 0.9, phastCons 1
Overall
CADD	7.437	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.877% Middle Eastern · 53/6,044 alleles

Filtering AF 0.745% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.74%

Overall 0.686% 10,923/1,592,592 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	1.67%	60
Middle Easterngrpmax	0.877%	114
Remaining individualsnot grpmax-eligible	0.78%	128
European (non-Finnish)	0.758%	132
Admixed American	0.564%	177
South Asian	0.546%	183
Finnishnot grpmax-eligible	0.241%	415
African / African-American	0.113%	888
East Asian	0.00454%	22,014

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: CAMSAP1
Protein: p.Ala1509=
Coding: c.4527C>G
MANE Select: NM_015447
Type: single nucleotide variant
Location: chr9:135811591 (GRCh38)
Gene constraint: LOEUF 0.544 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 55.21 · 4 PDB
Residue 1509: the ckk domain; a UniProt-annotated variant site (in cdcbm12)

Full CAMSAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CAMSAP1 p.Ser1398Ter Pathogenic/Likely pathogenic ★★ same type
CAMSAP1 p.Leu29Met Uncertain significance ★★ ⚠ same type
CAMSAP1 p.Ala914= Benign/Likely benign ★★ same type
CAMSAP1 p.Arg116Gln Likely benign ★★ same type
CAMSAP1 p.Asp556= Benign ★★ same type
CAMSAP1 p.Gly1399= Benign/Likely benign ★★ same type
CAMSAP1 p.Gly568= Likely benign ★★ same type
CAMSAP1 p.Ser811= Benign ★★ 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/camsap1-p-ala1509 (accessed [today's date]).

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