Is IPMK p.Gly15= (c.45C>T) pathogenic?

IPMK p.Gly15= (c.45C>T) is classified Likely benign in IPMK (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-12). Very rare (popmax 0.009%, nfe).

How common is IPMK p.Gly15= (c.45C>T) in the general population?

IPMK p.Gly15= (c.45C>T) is very rare (popmax 0.009%, nfe) (gnomAD).

IPMK p.Gly15=

c.45C>T · VCV4907483

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.009%, nfe)

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 0.19	GERP -2.4
Overall
CADD	5.008	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.009% European (non-Finnish) · 106/1,178,120 alleles

Filtering AF 0.00759% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00707%

Overall 0.00677% 109/1,609,070 alleles · very rare exomes 105/1,456,868 · genomes 4/152,202 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.009%	11,114
Admixed American	0.00168%	59,566
Remaining individualsnot grpmax-eligible	0.00161%	62,144
African / African-American	0.00134%	74,848

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: IPMK
Protein: p.Gly15=
Coding: c.45C>T
MANE Select: NM_152230
Type: single nucleotide variant
Location: chr10:58267567 (GRCh38)
Gene constraint: LOEUF 0.6 · pLI 0.82 (gnomAD)
Structure: AlphaFold pLDDT 74.50 · 25 PDB
Residue 15: the 'disordered' region

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

Similar variants

IPMK p.Asn124= Benign ★★ same type
IPMK p.Thr32= Benign ★★ same type
IPMK p.Ala228Val Uncertain significance ★ ⚠ same type
IPMK p.Ala250Thr Uncertain significance ★ ⚠ same type
IPMK p.Ala319Val Uncertain significance ★ ⚠ same type
IPMK p.Arg10Gln Uncertain significance ★ ⚠ same type
IPMK p.Arg10Trp Uncertain significance ★ ⚠ same type
IPMK p.Arg320His 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/ipmk-p-gly15 (accessed [today's date]).

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