KDM3B p.Pro348=
c.1044C>T · VCV4972151
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000339%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.35 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.85 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 9.101 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000339%
European (non-Finnish) · 4/1,180,048 alleles
Filtering AF
7.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.000248%
4/1,614,160 alleles · very rare
exomes 4/1,461,894 · genomes 0/152,266 · joint denominator
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
- KDM3B
- Protein
- p.Pro348=
- Coding
- c.1044C>T
- MANE Select
- NM_016604
- Type
- single nucleotide variant
- Location
- chr5:138386285 (GRCh38)
- Gene constraint
- LOEUF 0.117 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 59.78 · 36 PDB
- Residue 348
- a UniProt-annotated variant site (in dijos)
Similar variants
- KDM3B p.Pro348Ala Uncertain significance ★ ⚠ same residue
- KDM3B p.Pro348Leu Uncertain significance ★ ⚠ same residue
- KDM3B p.Ala1543Thr Likely pathogenic ★★ same type
- KDM3B p.Arg1472Ter Likely pathogenic ★★ same type
- KDM3B p.Arg1517Ter Pathogenic/Likely pathogenic ★★ same type
- KDM3B p.Arg943Gln Pathogenic/Likely pathogenic ★★ same type
- KDM3B p.Tyr1544Cys Pathogenic ★★ same type
- KDM3B p.Ala31Val 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/kdm3b-p-pro348 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown