CBS p.Met1Thr
c.2T>C · rs769766030 · VCV196204
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
Consequence
start-loss
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
HYPERHOMOCYSTEINEMIA, THROMBOTIC, CBS-RELATED
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | start-loss | predicted loss-of-function |
|---|---|---|
| REVEL | 0.601 | indeterminate |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 22.1 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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
- CBS
- Protein
- p.Met1Thr
- Coding
- c.2T>C
- MANE Select
- NM_000071
- dbSNP
- rs769766030
- Type
- single nucleotide variant
- Location
- chr21:43072192 (GRCh38)
- Structure
- AlphaFold pLDDT 90.15 · 28 PDB
- Residue 1
- the 'disordered' region
Similar variants
- CBS p.Met1Ile Likely pathogenic ★ same residue
- 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
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-met1thr (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown