Is KIF7 p.Ser462Phe (c.1384_1385delinsTT) pathogenic?

KIF7 p.Ser462Phe (c.13841385delinsTT) is classified Uncertain significance in KIF7 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-24). No gnomAD frequency available for this variant; Associated with acrocallosal syndrome.

What condition is associated with KIF7 p.Ser462Phe (c.1384_1385delinsTT)?

KIF7 p.Ser462Phe (c.1384_1385delinsTT) is associated with acrocallosal syndrome (ClinVar).

How common is KIF7 p.Ser462Phe (c.1384_1385delinsTT) in the general population?

KIF7 p.Ser462Phe (c.1384_1385delinsTT) is no gnomAD frequency available for this variant (gnomAD).

KIF7 p.Ser462Phe

c.1384_1385delinsTT · rs2505493216 · VCV2158391

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

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.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.4	GERP 1.9, phastCons 1
Regional constraint	o/e 1.09	unconstrained · MANE · 25 kb · p 0.00011 · regional, not allelic

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.Ser462Phe
Coding: c.1384_1385delinsTT
MANE Select: NM_198525
dbSNP: rs2505493216
Type: Indel
Location: chr15:89648313 (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 462: the 'interaction with smo' region; the 'interaction with dlg5' region; the 'disordered' region

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.Ser462Gly Uncertain significance ★ ⚠ same residue
KIF7 p.Glu979Ter Pathogenic ★ same condition
KIF7 c.2895+5_2895+6delinsTA Uncertain significance ★ same condition
KIF7 c.2896-14_2896-13delinsAC Uncertain significance ★ same condition
KIF7 c.924-7_924-5delinsGCT Uncertain significance ★ same condition
KIF7 p.Ala162Asn Uncertain significance ★ same condition
KIF7 p.Gln829_Leu830delinsHisPhe Uncertain significance ★ same condition
KIF7 p.Glu367_Thr368delinsAspAla Uncertain significance ★ 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-ser462phe (accessed [today's date]).

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