KIF7 p.Phe83=
c.249C>T · rs1293359223 · VCV2737899
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00238%, sas)
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 0.55 | GERP -5.1, phastCons 0.91 |
| Overall | ||
| CADD | 8.616 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00238%
South Asian · 2/84,026 alleles
Filtering AF
0.000395%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000148%
Overall
0.000193%
3/1,551,336 alleles · very rare
exomes 3/1,399,000 · genomes 0/152,336 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00238% | 42,013 |
| European (non-Finnish) | 8.72e-05% | 1,146,572 |
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
- KIF7
- Protein
- p.Phe83=
- Coding
- c.249C>T
- MANE Select
- NM_198525
- dbSNP
- rs1293359223
- Type
- single nucleotide variant
- Location
- chr15:89652682 (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 83
- the kinesin motor domain; an α-helix
Similar variants
- KIF7 p.Phe83Leu Uncertain significance ★★ ⚠ same residue
- KIF7 p.Phe83Val Uncertain significance ★★ same residue
- 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
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-phe83 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown