KIFBP p.Pro463=
c.1389A>C · rs114205227 · VCV387423
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.41%, afr)
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 -2.1 | GERP -3.5 |
| Overall | ||
| CADD | 2.408 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.41%
African / African-American · 1,062/75,060 alleles
Filtering AF
1.34%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.32%
Overall
0.0784%
1,265/1,614,208 alleles · low-frequency
exomes 607/1,461,878 · genomes 658/152,330 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.41% | 71 |
| Admixed American | 0.145% | 690 |
| Remaining individualsnot grpmax-eligible | 0.107% | 933 |
| Middle Eastern | 0.099% | 1,010 |
| European (non-Finnish) | 0.00347% | 28,781 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,604 |
| South Asian | 0.0011% | 91,086 |
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
- KIFBP
- Protein
- p.Pro463=
- Coding
- c.1389A>C
- MANE Select
- NM_015634
- dbSNP
- rs114205227
- Type
- single nucleotide variant
- Location
- chr10:69015939 (GRCh38)
- Gene constraint
- LOEUF 1.016 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.76 · 6 PDB
Similar variants
- KIFBP p.Ser200Ter Pathogenic ★★ same type
- KIFBP p.Ala243Gly Uncertain significance ★★ ⚠ same type
- KIFBP p.Ala39Gly Uncertain significance ★★ same type
- KIFBP p.Ala490Thr Uncertain significance ★★ ⚠ same type
- KIFBP p.Ala590Thr Uncertain significance ★★ ⚠ same type
- KIFBP p.Arg237His Uncertain significance ★★ ⚠ same type
- KIFBP p.Arg359Gln Uncertain significance ★★ ⚠ same type
- KIFBP p.Arg442Thr 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/kifbp-p-pro463 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown