KDM5B p.Ser1271=
c.3813G>A · rs185116953 · VCV2639793
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.167%, eas)
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 -12 | GERP -3.7 |
| Overall | ||
| CADD | 0.182 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.167%
East Asian · 75/44,876 alleles
Filtering AF
0.137%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.125%
Overall
0.00966%
156/1,614,124 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.167% | 598 |
| Remaining individualsnot grpmax-eligible | 0.088% | 1,137 |
| South Asian | 0.0165% | 6,072 |
| African / African-American | 0.004% | 25,015 |
| Admixed American | 0.00333% | 30,004 |
| European (non-Finnish) | 0.000508% | 196,668 |
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
- KDM5B
- Protein
- p.Ser1271=
- Coding
- c.3813G>A
- MANE Select
- NM_006618
- dbSNP
- rs185116953
- Type
- single nucleotide variant
- Location
- chr1:202733497 (GRCh38)
- Gene constraint
- LOEUF 0.858 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 72.52 · 56 PDB
- Residue 1271
- a UniProt-annotated variant site (in mrt65)
Similar variants
- KDM5B c.2945+1G>A Likely pathogenic ★★ same type
- KDM5B p.Arg1047Ter Pathogenic/Likely pathogenic ★★ same type
- KDM5B p.Arg1214Ter Likely pathogenic ★★ same type
- KDM5B p.Arg1253Ter Pathogenic/Likely pathogenic ★★ same type
- KDM5B p.Arg1281Ter Pathogenic/Likely pathogenic ★★ same type
- KDM5B p.Arg1426Ter Pathogenic/Likely pathogenic ★★ same type
- KDM5B p.Arg259Ter Pathogenic/Likely pathogenic ★★ same type
- KDM5B p.Arg299Ter Pathogenic/Likely pathogenic ★★ 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/kdm5b-p-ser1271 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown