Is CAMSAP1 p.Lys1366Arg (c.4097A>G) pathogenic?

CAMSAP1 p.Lys1366Arg (c.4097A>G) is classified Likely benign in CAMSAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-06). AlphaMissense: likely benign (0.0578); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CAMSAP1 p.Lys1366Arg (c.4097A>G)?

CAMSAP1 p.Lys1366Arg (c.4097A>G) is associated with Inborn genetic diseases (ClinVar).

How common is CAMSAP1 p.Lys1366Arg (c.4097A>G) in the general population?

CAMSAP1 p.Lys1366Arg (c.4097A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CAMSAP1 p.Lys1366Arg (c.4097A>G)?

AlphaMissense predicts likely benign (score 0.0578) — an in-silico prediction, not a clinical call.

CAMSAP1 p.Lys1366Arg

c.4097A>G · VCV4218533

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0578 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0578	likely benign
REVEL	0.097	moderately benign-leaning
SaProt	LLR -6.72	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 0.12	GERP -3.9
Regional constraint	o/e 0.98	unconstrained · MANE · 12 kb · p 0.41 · regional, not allelic
Overall
CADD	6.085	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CAMSAP1
Protein: p.Lys1366Arg
Coding: c.4097A>G
MANE Select: NM_015447
Type: single nucleotide variant
Location: chr9:135818479 (GRCh38)
Gene constraint: LOEUF 0.544 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 55.21 · 4 PDB
Residue 1366: the 'disordered' region; 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-lys1366arg (accessed [today's date]).

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