Is CAMSAP1 p.Ser671Leu (c.2012C>T) pathogenic?

CAMSAP1 p.Ser671Leu (c.2012C>T) is classified Uncertain significance in CAMSAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-17). AlphaMissense: likely benign (0.0677); Ultra-rare (popmax 0.0504%, amr); Associated with Inborn genetic diseases.

What condition is associated with CAMSAP1 p.Ser671Leu (c.2012C>T)?

CAMSAP1 p.Ser671Leu (c.2012C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CAMSAP1 p.Ser671Leu (c.2012C>T) in the general population?

CAMSAP1 p.Ser671Leu (c.2012C>T) is ultra-rare (popmax 0.0504%, amr) (gnomAD).

What do computational predictors say about CAMSAP1 p.Ser671Leu (c.2012C>T)?

AlphaMissense predicts likely benign (score 0.0677) — an in-silico prediction, not a clinical call.

CAMSAP1 p.Ser671Leu

c.2012C>T · rs559798666 · VCV2351489

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0677 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0504%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0677	likely benign
REVEL	0.079	moderately benign-leaning
SaProt	LLR -6.39	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 0.054	GERP -2.1
Regional constraint	o/e 0.98	unconstrained · MANE · 12 kb · p 0.41 · regional, not allelic
Overall
CADD	8.258	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 0.0504% Admixed American · 30/59,574 alleles

Filtering AF 0.0362% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0314%

Overall 0.00665% 107/1,609,886 alleles · ultra-rare exomes 90/1,457,702 · genomes 17/152,184 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0504%	1,986
Middle Eastern	0.0498%	2,008
Remaining individualsnot grpmax-eligible	0.0305%	3,276
European (non-Finnish)	0.00442%	22,643
African / African-American	0.00267%	37,392
South Asian	0.0011%	90,940

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.Ser671Leu
Coding: c.2012C>T
MANE Select: NM_015447
dbSNP: rs559798666
Type: single nucleotide variant
Location: chr9:135822649 (GRCh38)
Gene constraint: LOEUF 0.544 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 55.21 · 4 PDB
Residue 671: 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-ser671leu (accessed [today's date]).

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