CGN p.Met289Val
c.865A>G · rs146676976 · VCV2367240
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00902%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.084 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.2 | GERP -4.9 |
| Regional constraint | o/e 0.97 | unconstrained · MANE · 16 kb · p 0.38 · regional, not allelic |
| Overall | ||
| CADD | 0.096 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00902%
European (non-Finnish) · 106/1,174,808 alleles
Filtering AF
0.00761%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00709%
Overall
0.00704%
112/1,590,486 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00902% | 11,083 |
| Remaining individualsnot grpmax-eligible | 0.00322% | 31,018 |
| African / African-American | 0.00268% | 37,334 |
| Finnishnot grpmax-eligible | 0.00198% | 50,568 |
| Admixed American | 0.00173% | 57,856 |
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
- CGN
- Protein
- p.Met289Val
- Coding
- c.865A>G
- MANE Select
- NM_020770
- dbSNP
- rs146676976
- Type
- single nucleotide variant
- Location
- chr1:151519384 (GRCh38)
- Gene constraint
- LOEUF 0.88 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.44
- Residue 289
- the 'head' region
Similar variants
- CGN p.Ala357= Benign/Likely benign ★★ same type
- CGN p.Arg11Trp Likely benign ★★ same type
- CGN p.Arg227Trp Likely benign ★★ same type
- CGN p.Arg547Lys Benign ★★ same type
- CGN p.Arg973Gln Benign ★★ same type
- CGN p.Glu771Lys Benign/Likely benign ★★ same type
- CGN p.Ile60= Benign ★★ same type
- CGN p.Ala1035Thr Uncertain significance ★ same type
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/cgn-p-met289val (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown