KIZ p.Pro284=
c.852A>G · rs2122692269 · VCV1616679
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 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.37 | GERP -4.7, phastCons 0.59 |
| Overall | ||
| CADD | 6.673 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000339%
European (non-Finnish) · 4/1,179,812 alleles
Filtering AF
7.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.000248%
4/1,613,934 alleles · very rare
exomes 4/1,461,576 · genomes 0/152,358 · 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
- KIZ
- Protein
- p.Pro284=
- Coding
- c.852A>G
- MANE Select
- NM_018474
- dbSNP
- rs2122692269
- Type
- single nucleotide variant
- Location
- chr20:21162317 (GRCh38)
- Gene constraint
- LOEUF 1.227 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.82
- Residue 284
- the 'disordered' region
Similar variants
- KIZ c.1447-2A>G Likely pathogenic ★★ same type
- KIZ c.1612+2T>G Likely pathogenic ★★ same type
- KIZ p.Arg195Ter Pathogenic/Likely pathogenic ★★ same type
- KIZ p.Arg76Ter Pathogenic ★★ same type
- KIZ p.Gln199Ter Pathogenic/Likely pathogenic ★★ same type
- KIZ p.Gln22Ter Pathogenic/Likely pathogenic ★★ same type
- KIZ p.Glu18Ter Pathogenic/Likely pathogenic ★★ same type
- KIZ p.Leu625Ter 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/kiz-p-pro284 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown