CUBN c.348+17C>T
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.244%, amr)
Conditions
1
Imerslund-Grasbeck syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +17 | near-intronic (+17 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.66 | GERP -1.3 |
| Overall | ||
| CADD | 4.321 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.244%
Admixed American · 146/59,918 alleles
Filtering AF
0.211%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.199%
Overall
0.16%
2,537/1,581,028 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.244% | 410 |
| European (non-Finnish) | 0.198% | 506 |
| Remaining individualsnot grpmax-eligible | 0.132% | 759 |
| Middle Eastern | 0.05% | 2,001 |
| African / African-American | 0.0336% | 2,973 |
| Finnishnot grpmax-eligible | 0.00626% | 15,965 |
| South Asian | 0.00443% | 22,578 |
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
- Coding
- c.348+17C>T
- MANE Select
- NM_001081
- dbSNP
- rs200466568
- Type
- single nucleotide variant
- Location
- chr10:17127812 (GRCh38)
- Gene constraint
- LOEUF 0.756 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
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 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-c-348-plus-17c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown