Is CAMSAP1 p.Asp3Glu (c.9C>G) pathogenic?

CAMSAP1 p.Asp3Glu (c.9C>G) is classified Uncertain significance in CAMSAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-28). AlphaMissense: ambiguous (0.4589); Very rare (popmax 0.00486%, nfe); Associated with Inborn genetic diseases.

What condition is associated with CAMSAP1 p.Asp3Glu (c.9C>G)?

CAMSAP1 p.Asp3Glu (c.9C>G) is associated with Inborn genetic diseases (ClinVar).

How common is CAMSAP1 p.Asp3Glu (c.9C>G) in the general population?

CAMSAP1 p.Asp3Glu (c.9C>G) is very rare (popmax 0.00486%, nfe) (gnomAD).

What do computational predictors say about CAMSAP1 p.Asp3Glu (c.9C>G)?

AlphaMissense predicts ambiguous (score 0.4589) — an in-silico prediction, not a clinical call.

CAMSAP1 p.Asp3Glu

c.9C>G · VCV4604502

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4589 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00486%, nfe)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.4589	ambiguous
REVEL	0.021	moderately benign-leaning
SaProt	LLR -5.08	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.7	GERP 0.32, phastCons 1
Regional constraint	o/e 1.10	unconstrained · MANE · 25 kb · p 0.18 · regional, not allelic
Overall
CADD	22.2	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

Grpmax group 0.00486% European (non-Finnish) · 44/905,002 alleles

Filtering AF 0.00368% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00328%

Overall 0.00398% 44/1,104,970 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: CAMSAP1
Protein: p.Asp3Glu
Coding: c.9C>G
MANE Select: NM_015447
Type: single nucleotide variant
Location: chr9:135907151 (GRCh38)
Gene constraint: LOEUF 0.544 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 55.21 · 4 PDB

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-asp3glu (accessed [today's date]).

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