Is KIF7 p.Ile299fs (c.895del) pathogenic?

KIF7 p.Ile299fs (c.895del) is classified Pathogenic in KIF7 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-08). No gnomAD frequency available for this variant; Associated with acrocallosal syndrome.

What condition is associated with KIF7 p.Ile299fs (c.895del)?

KIF7 p.Ile299fs (c.895del) is associated with acrocallosal syndrome (ClinVar).

How common is KIF7 p.Ile299fs (c.895del) in the general population?

KIF7 p.Ile299fs (c.895del) is no gnomAD frequency available for this variant (gnomAD).

KIF7 p.Ile299fs

c.895del · rs2505498070 · VCV2018195

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

acrocallosal syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 4 of 19
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.6, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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.Ile299fs
Coding: c.895del
MANE Select: NM_198525
dbSNP: rs2505498070
Type: Deletion
Location: chr15:89649002 (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 299: the kinesin motor domain

Full KIF7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

acrocallosal syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

KIF7 p.Ala369fs Pathogenic/Likely pathogenic ★★ same condition
KIF7 p.Ala854fs Pathogenic/Likely pathogenic ★★ same condition
KIF7 p.Ala966fs Pathogenic ★★ same condition
KIF7 p.Asp417fs Pathogenic/Likely pathogenic ★★ same condition
KIF7 p.Arg1329_Ser1332del Uncertain significance ★★ same condition
KIF7 p.Leu1254_Pro1259del Uncertain significance ★★ same condition
KIF7 p.Leu1343fs Uncertain significance ★★ same condition
KIF7 p.Ala11fs 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-ile299fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown