CUBN p.Pro2575=
c.7725A>C · rs1841558814 · VCV2811302
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
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 0.17 | GERP -3.7, phastCons 0.003 |
| Overall | ||
| CADD | 0.583 | PHRED · no single calibrated threshold — expert panels disagree |
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
- CUBN
- Protein
- p.Pro2575=
- Coding
- c.7725A>C
- MANE Select
- NM_001081
- dbSNP
- rs1841558814
- Type
- single nucleotide variant
- Location
- chr10:16906390 (GRCh38)
- Gene constraint
- LOEUF 0.756 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 2575
- a UniProt-annotated variant site (in prochob); a UniProt-annotated variant site (in); the cub 19 domain
Disease context
Imerslund-Grasbeck syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Imerslund-Gräsbeck syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood
- Prevalence
- 1-9 / 1 000 000 (Finland)
Similar variants
- CUBN p.Pro2575Arg Benign ★★ same residue
- 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
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-pro2575 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown