CUBN p.Val2232=
c.6696G>A · rs1039114405 · VCV2959664
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00401%, afr)
Conditions
2
Inborn genetic diseases
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 1.7 | GERP -0.33, phastCons 1 |
| Overall | ||
| CADD | 8.745 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00401%
African / African-American · 3/74,848 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000495%
Overall
0.000186%
3/1,613,768 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
- CUBN
- Protein
- p.Val2232=
- Coding
- c.6696G>A
- MANE Select
- NM_001081
- dbSNP
- rs1039114405
- Type
- single nucleotide variant
- Location
- chr10:16920088 (GRCh38)
- Gene constraint
- LOEUF 0.756 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 2232
- a disulfide bond; a UniProt-annotated variant site (in prochob); the cub 16 domain
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-val2232 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown