KIF7 p.Phe55=
c.165T>C · rs1011116318 · VCV1628974
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0333%, mid)
Conditions
1
acrocallosal syndrome
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 -1.3 | GERP -4.8 |
| Overall | ||
| CADD | 3.633 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0333%
Middle Eastern · 2/6,008 alleles
Filtering AF
0.00587%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00244%
Overall
0.000645%
10/1,551,508 alleles · ultra-rare
exomes 7/1,399,254 · genomes 3/152,254 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0333% | 3,004 |
| East Asian | 0.00733% | 13,644 |
| Remaining individualsnot grpmax-eligible | 0.00166% | 60,096 |
| European (non-Finnish) | 0.000349% | 286,744 |
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.Phe55=
- Coding
- c.165T>C
- MANE Select
- NM_198525
- dbSNP
- rs1011116318
- Type
- single nucleotide variant
- Location
- chr15:89652766 (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 55
- the kinesin motor domain; a β-strand
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-phe55 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown