KIF7 p.Pro392=
c.1176A>G · rs1964060075 · VCV1569663
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000217%, nfe)
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 -3.7 | GERP -3.8 |
| Overall | ||
| CADD | 2.196 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000217%
European (non-Finnish) · 2/922,534 alleles
Filtering AF
3.6e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.4e-05%
Overall
0.000176%
2/1,133,670 alleles · very rare
exomes 1/987,130 · genomes 1/146,540 · 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
- KIF7
- Protein
- p.Pro392=
- Coding
- c.1176A>G
- MANE Select
- NM_198525
- dbSNP
- rs1964060075
- Type
- single nucleotide variant
- Location
- chr15:89648522 (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 392
- the 'interaction with smo' region; the 'interaction with dlg5' region
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-pro392 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown