CBS p.Ile240=
c.720C>A · rs769024492 · VCV793836
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000395%, nfe)
Conditions
1
HYPERHOMOCYSTEINEMIA, THROMBOTIC, CBS-RELATED
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 1.4 | GERP -2.2, phastCons 1 |
| Overall | ||
| CADD | 5.941 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000395%
European (non-Finnish) · 4/1,013,450 alleles
Filtering AF
9.2e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.2e-05%
Overall
0.000284%
4/1,409,972 alleles · very rare
exomes 4/1,283,692 · genomes 0/126,280 · joint denominator
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
- CBS
- Protein
- p.Ile240=
- Coding
- c.720C>A
- MANE Select
- NM_000071
- dbSNP
- rs769024492
- Type
- single nucleotide variant
- Location
- chr21:43065219 (GRCh38)
- Structure
- AlphaFold pLDDT 90.15 · 28 PDB
- Residue 240
- an α-helix
Similar variants
- CBS c.1145+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CBS c.1223+1G>T Pathogenic ★★ same condition
- CBS c.1552+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CBS c.451+1G>T Likely pathogenic ★★ same condition
- CBS c.531+1G>A Likely pathogenic ★★ same condition
- CBS c.736+2T>G Pathogenic ★★ same condition
- CBS c.954+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CBS p.Ala226Thr 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/cbs-p-ile240 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown