MLST8 p.Pro230=
c.690C>G · rs202083987 · VCV2524973
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.124%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -15 | GERP -3.6 |
| Overall | ||
| CADD | 0.086 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.124%
European (non-Finnish) · 1,454/1,174,884 alleles
Filtering AF
0.118%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.116%
Overall
0.0942%
1,513/1,606,820 alleles · rare
exomes 1,433/1,454,584 · genomes 80/152,236 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.124% | 808 |
| Remaining individualsnot grpmax-eligible | 0.0628% | 1,593 |
| Middle Eastern | 0.0495% | 2,020 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0136% | 7,372 |
| African / African-American | 0.0134% | 7,473 |
| Admixed American | 0.00336% | 29,802 |
| South Asian | 0.0011% | 90,956 |
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
- MLST8
- Protein
- p.Pro230=
- Coding
- c.690C>G
- MANE Select
- NM_022372
- dbSNP
- rs202083987
- Type
- single nucleotide variant
- Location
- chr16:2208326 (GRCh38)
- Gene constraint
- LOEUF 0.679 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 92.15 · 45 PDB
Similar variants
- MLST8 p.Pro230Leu Uncertain significance ★ ⚠ same residue
- MLST8 p.Ala223Thr Uncertain significance ★ ⚠ same type
- MLST8 p.Arg221Cys Uncertain significance ★ same type
- MLST8 p.Arg227Cys Uncertain significance ★ ⚠ same type
- MLST8 p.Arg227His Uncertain significance ★ ⚠ same type
- MLST8 p.Arg25His Uncertain significance ★ ⚠ same type
- MLST8 p.Arg66Leu Uncertain significance ★ ⚠ same type
- MLST8 p.Asn132Lys 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/mlst8-p-pro230 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown