KMO p.Pro262=
c.786G>A · rs142152979 · VCV771693
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.28%, nfe)
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 -1.7 | GERP -3.5 |
| Overall | ||
| CADD | 6.654 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.28%
European (non-Finnish) · 15,115/1,179,680 alleles
Filtering AF
1.26%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.26%
Overall
1%
16,128/1,613,574 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.28% | 78 |
| Remaining individualsnot grpmax-eligible | 0.629% | 159 |
| Admixed American | 0.412% | 243 |
| Ashkenazi Jewishnot grpmax-eligible | 0.264% | 379 |
| African / African-American | 0.187% | 536 |
| Finnishnot grpmax-eligible | 0.183% | 547 |
| Middle Eastern | 0.099% | 1,010 |
| South Asian | 0.0352% | 2,844 |
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
- KMO
- Protein
- p.Pro262=
- Coding
- c.786G>A
- MANE Select
- NM_003679
- dbSNP
- rs142152979
- Type
- single nucleotide variant
- Location
- chr1:241566589 (GRCh38)
- Gene constraint
- LOEUF 0.755 · pLI 0.15 (gnomAD)
- Structure
- AlphaFold pLDDT 88.56 · 1 PDB
Similar variants
- KMO p.Pro262Leu Likely benign ★ ⚠ same residue
- KMO p.Val253Met Uncertain significance ★★ ⚠ same type
- KMO c.957+9T>A Benign ★★ same type
- KMO c.223-1G>T Uncertain significance ★ same type
- KMO p.Arg182Gly Uncertain significance ★ ⚠ same type
- KMO p.Arg40Thr Uncertain significance ★ ⚠ same type
- KMO p.Arg414Cys Uncertain significance ★ ⚠ same type
- KMO p.Arg63Gln 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/kmo-p-pro262 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown