Is CUBN p.Asp2433= (c.7299C>T) pathogenic?

CUBN p.Asp2433= (c.7299C>T) is classified Likely benign in CUBN (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-09-16). Ultra-rare (popmax 0.0668%, eas); Associated with Imerslund-Grasbeck syndrome.

What condition is associated with CUBN p.Asp2433= (c.7299C>T)?

CUBN p.Asp2433= (c.7299C>T) is associated with Imerslund-Grasbeck syndrome (ClinVar).

How common is CUBN p.Asp2433= (c.7299C>T) in the general population?

CUBN p.Asp2433= (c.7299C>T) is ultra-rare (popmax 0.0668%, eas) (gnomAD).

How is Imerslund-Gräsbeck syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

CUBN p.Asp2433=

c.7299C>T · rs201002903 · VCV697182

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0668%, eas)

Conditions

Imerslund-Grasbeck syndrome

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 -0.99	GERP -3
Overall
CADD	2.207	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0668% East Asian · 30/44,892 alleles

Filtering AF 0.0481% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0417%

Overall 0.00682% 110/1,613,856 alleles · ultra-rare exomes 95/1,461,690 · genomes 15/152,166 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0668%	1,496
Middle Eastern	0.0331%	3,025
Remaining individualsnot grpmax-eligible	0.0112%	8,925
European (non-Finnish)	0.00525%	19,031
Finnishnot grpmax-eligible	0.00469%	21,344
Admixed American	0.00333%	29,997
South Asian	0.00329%	30,361
African / African-American	0.00134%	74,902

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: CUBN
Protein: p.Asp2433=
Coding: c.7299C>T
MANE Select: NM_001081
dbSNP: rs201002903
Type: single nucleotide variant
Location: chr10:16915084 (GRCh38)
Gene constraint: LOEUF 0.756 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 2433: a UniProt-annotated variant site (in prochob); the cub 17 domain

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

Disease context

Imerslund-Grasbeck syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Imerslund-Gräsbeck syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood
Prevalence: 1-9 / 1 000 000 (Finland)

Similar variants

CUBN c.10033-1G>A Likely pathogenic ★★ same condition
CUBN c.1230+1G>A Pathogenic/Likely pathogenic ★★ same condition
CUBN c.3829+1G>A Pathogenic/Likely pathogenic ★★ same condition
CUBN c.4350+2T>C Likely pathogenic ★★ same condition
CUBN c.6822-1G>A Likely pathogenic ★★ same condition
CUBN c.8598+1G>T Likely pathogenic ★★ same condition
CUBN c.9454+1G>A Likely pathogenic ★★ same condition
CUBN p.Arg1487Ter 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/cubn-p-asp2433 (accessed [today's date]).

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