KIF7 p.Leu289=
c.867G>A · rs2505498283 · VCV2709396
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,548,394)
Conditions
1
acrocallosal syndrome
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 | GERP -4.8, phastCons 1 |
| Overall | ||
| CADD | 8.162 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,548,394). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- KIF7
- Protein
- p.Leu289=
- Coding
- c.867G>A
- MANE Select
- NM_198525
- dbSNP
- rs2505498283
- Type
- single nucleotide variant
- Location
- chr15:89649030 (GRCh38)
- Gene constraint
- LOEUF 1.038 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 68.07 · 5 PDB
- Residue 289
- the kinesin motor domain; an α-helix
Similar variants
- KIF7 c.1443+2T>C Likely pathogenic ★★ same condition
- KIF7 c.1561-1G>A Likely pathogenic ★★ same condition
- KIF7 c.1789-2A>G Likely pathogenic ★★ same condition
- KIF7 c.2593-3C>G Pathogenic ★★ same condition
- KIF7 c.328+2T>G Pathogenic/Likely pathogenic ★★ same condition
- KIF7 c.3518-1G>C Likely pathogenic ★★ same condition
- KIF7 c.923+2T>G Likely pathogenic ★★ same condition
- KIF7 p.Arg1111Ter Pathogenic ★★ same condition
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/kif7-p-leu289 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown