Is CCM2 p.Asn401= (c.1203T>C) pathogenic?

CCM2 p.Asn401= (c.1203T>C) is classified Benign/Likely benign in CCM2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-10-26). Rare (popmax 0.234%, eas); Associated with cerebral cavernous malformation 2.

What condition is associated with CCM2 p.Asn401= (c.1203T>C)?

CCM2 p.Asn401= (c.1203T>C) is associated with cerebral cavernous malformation 2 (ClinVar).

How common is CCM2 p.Asn401= (c.1203T>C) in the general population?

CCM2 p.Asn401= (c.1203T>C) is rare (popmax 0.234%, eas) (gnomAD).

CCM2 p.Asn401=

c.1203T>C · rs367740781 · VCV706367

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.234%, eas)

Conditions

cerebral cavernous malformation 2

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 -15	GERP -2.6
Overall
CADD	0.102	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.234% East Asian · 105/44,876 alleles

Filtering AF 0.198% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.184%

Overall 0.00738% 119/1,612,904 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.234%	427
Remaining individualsnot grpmax-eligible	0.0128%	7,810
Admixed American	0.00167%	59,986
South Asian	0.0011%	91,066
European (non-Finnish)	0.000339%	294,990

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: CCM2
Protein: p.Asn401=
Coding: c.1203T>C
MANE Select: NM_031443
dbSNP: rs367740781
Type: single nucleotide variant
Location: chr7:45075925 (GRCh38)
Gene constraint: LOEUF 0.753 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.48 · 8 PDB
Residue 401: the 'disordered' region

Full CCM2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

cerebral cavernous malformation 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CCM2 p.Asn401Asp Uncertain significance ★ ⚠ same residue
CCM2 c.289-1G>A Pathogenic/Likely pathogenic ★★ same condition
CCM2 c.30+1G>A Pathogenic ★★ same condition
CCM2 c.472+1G>C Pathogenic/Likely pathogenic ★★ same condition
CCM2 c.473-1G>T Pathogenic ★★ same condition
CCM2 c.745+1G>T Pathogenic ★★ same condition
CCM2 p.Arg19Ter Pathogenic ★★ same condition
CCM2 p.Arg57Ter Pathogenic/Likely pathogenic ★★ 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/ccm2-p-asn401 (accessed [today's date]).

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