Is KIF23 p.Pro9= (c.27C>T) pathogenic?

KIF23 p.Pro9= (c.27C>T) is classified Likely benign in KIF23 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-07-06). No allele count reported in gnomAD v4.1 (AN 1,579,330).

How common is KIF23 p.Pro9= (c.27C>T) in the general population?

KIF23 p.Pro9= (c.27C>T) is no allele count reported in gnomAD v4.1 (AN 1,579,330) (gnomAD).

KIF23 p.Pro9=

c.27C>T · rs1595972244 · VCV754232

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,579,330)

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 -0.02	GERP 3.3, phastCons 0.79
Overall
CADD	6.86	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,579,330). 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: KIF23
Protein: p.Pro9=
Coding: c.27C>T
MANE Select: NM_001367805
dbSNP: rs1595972244
Type: single nucleotide variant
Location: chr15:69416009 (GRCh38)
Gene constraint: LOEUF 0.279 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 73.08 · 1 PDB
Residue 9: the 'disordered' region

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-pro9 (accessed [today's date]).

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