Is KIF23 p.Phe239= (c.717T>C) pathogenic?

KIF23 p.Phe239= (c.717T>C) is classified Likely benign in KIF23 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-11). Absent from gnomAD v4.1.

How common is KIF23 p.Phe239= (c.717T>C) in the general population?

KIF23 p.Phe239= (c.717T>C) is absent from gnomAD v4.1 (gnomAD).

KIF23 p.Phe239=

c.717T>C · VCV4925665

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 1.6	GERP -0.47, phastCons 1
Overall
CADD	10.2	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: KIF23
Protein: p.Phe239=
Coding: c.717T>C
MANE Select: NM_001367805
Type: single nucleotide variant
Location: chr15:69423312 (GRCh38)
Gene constraint: LOEUF 0.279 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 73.08 · 1 PDB
Residue 239: the kinesin motor domain

Full KIF23 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

KIF23 c.1930-3T>C Uncertain significance ★★ same type
KIF23 p.Ala330Thr Uncertain significance ★★ ⚠ same type
KIF23 p.Ala816Thr Uncertain significance ★★ ⚠ same type
KIF23 p.Arg134Cys Uncertain significance ★★ ⚠ same type
KIF23 p.Arg173Cys Uncertain significance ★★ ⚠ same type
KIF23 p.Arg173His Uncertain significance ★★ ⚠ same type
KIF23 p.Arg310Cys Uncertain significance ★★ ⚠ same type
KIF23 p.Arg467Lys Uncertain significance ★★ ⚠ same type

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/kif23-p-phe239 (accessed [today's date]).

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