MET p.Ser213=
c.639G>A · rs587780738 · VCV135973
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00678%, nfe)
Conditions
2
renal cell carcinoma
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 -20 | GERP -3.7 |
| Overall | ||
| CADD | 0.012 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00678%
European (non-Finnish) · 80/1,179,974 alleles
Filtering AF
0.00554%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00514%
Overall
0.00527%
85/1,613,914 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00678% | 14,750 |
| East Asian | 0.00445% | 22,449 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,604 |
| Finnishnot grpmax-eligible | 0.00156% | 64,004 |
| South Asian | 0.0011% | 91,078 |
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
- MET
- Protein
- p.Ser213=
- Coding
- c.639G>A
- MANE Select
- NM_000245
- dbSNP
- rs587780738
- Type
- single nucleotide variant
- Location
- chr7:116699723 (GRCh38)
- Gene constraint
- LOEUF 0.446 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.28 · 130 PDB
- Residue 213
- a β-strand; the sema domain
Similar variants
- MET p.Ser213Leu Uncertain significance ★★ ⚠ same residue
- MET p.His1094Arg Pathogenic/Likely pathogenic ★★ ⚠ same condition
- MET p.Met1131Thr Pathogenic/Likely pathogenic ★★ same condition
- MET p.Val1092Ile Pathogenic/Likely pathogenic ★★ same condition
- MET p.Val1220Ile Pathogenic/Likely pathogenic ★★ same condition
- MET c.1200+2T>C Uncertain significance ★★ same condition
- MET c.1392+1G>T Uncertain significance ★★ same condition
- MET c.1392+3A>G Uncertain significance ★★ 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/met-p-ser213 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown