Is CAMSAP1 p.Cys679Ser (c.2036G>C) pathogenic?

CAMSAP1 p.Cys679Ser (c.2036G>C) is classified Uncertain significance in CAMSAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-01). AlphaMissense: likely benign (0.0768); Ultra-rare (popmax 0.0165%, mid); Associated with Inborn genetic diseases.

What condition is associated with CAMSAP1 p.Cys679Ser (c.2036G>C)?

CAMSAP1 p.Cys679Ser (c.2036G>C) is associated with Inborn genetic diseases (ClinVar).

How common is CAMSAP1 p.Cys679Ser (c.2036G>C) in the general population?

CAMSAP1 p.Cys679Ser (c.2036G>C) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

What do computational predictors say about CAMSAP1 p.Cys679Ser (c.2036G>C)?

AlphaMissense predicts likely benign (score 0.0768) — an in-silico prediction, not a clinical call.

CAMSAP1 p.Cys679Ser

c.2036G>C · VCV3484529

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0768 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0768	likely benign
REVEL	0.014	strongly benign-leaning
SaProt	LLR -4.66	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 -2.3	GERP -3.1
Regional constraint	o/e 0.98	unconstrained · MANE · 12 kb · p 0.41 · regional, not allelic
Overall
CADD	0.928	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

Grpmax group 0.0165% Middle Eastern · 1/6,072 alleles

Filtering AF 0.00817% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00634%

Overall 0.00155% 25/1,612,244 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,072
African / African-American	0.0147%	6,799
Ashkenazi Jewishnot grpmax-eligible	0.0135%	7,386
Remaining individualsnot grpmax-eligible	0.0016%	62,376
European (non-Finnish)	0.000679%	147,382

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.Cys679Ser
Coding: c.2036G>C
MANE Select: NM_015447
Type: single nucleotide variant
Location: chr9:135822625 (GRCh38)
Gene constraint: LOEUF 0.544 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 55.21 · 4 PDB
Residue 679: a UniProt-annotated variant site (in cdcbm12)

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CAMSAP1 p.Leu29Met Uncertain significance ★★ ⚠ same condition
CAMSAP1 c.4387+6G>A Uncertain significance ★ same condition
CAMSAP1 p.Ala1105Val Uncertain significance ★ ⚠ same condition
CAMSAP1 p.Ala1243Val Uncertain significance ★ ⚠ same condition
CAMSAP1 p.Ala1323Val Uncertain significance ★ ⚠ same condition
CAMSAP1 p.Ala1405Thr Uncertain significance ★ ⚠ same condition
CAMSAP1 p.Ala1405Val Uncertain significance ★ same condition
CAMSAP1 p.Ala1452Gly Uncertain significance ★ ⚠ same condition

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-cys679ser (accessed [today's date]).

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