Is IPMK p.Leu9His (c.26T>A) pathogenic?

IPMK p.Leu9His (c.26T>A) is classified Uncertain significance in IPMK (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-06). AlphaMissense: likely benign (0.1226); Very rare (popmax 0.00339%, amr).

How common is IPMK p.Leu9His (c.26T>A) in the general population?

IPMK p.Leu9His (c.26T>A) is very rare (popmax 0.00339%, amr) (gnomAD).

What do computational predictors say about IPMK p.Leu9His (c.26T>A)?

AlphaMissense predicts likely benign (score 0.1226) — an in-silico prediction, not a clinical call.

IPMK p.Leu9His

c.26T>A · VCV4039131

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1226 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00339%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1226	likely benign
REVEL	0.015	strongly benign-leaning
SaProt	LLR -7.86	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.6	GERP 1.2, phastCons 1
Regional constraint	o/e 1.11	unconstrained · MANE · 30 kb · p 0.27 · regional, not allelic
Overall
CADD	20.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00339% Admixed American · 2/58,968 alleles

Filtering AF 0.000563% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000211%

Overall 0.000125% 2/1,603,980 alleles · very rare

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.Leu9His
Coding: c.26T>A
MANE Select: NM_152230
Type: single nucleotide variant
Location: chr10:58267586 (GRCh38)
Gene constraint: LOEUF 0.6 · pLI 0.82 (gnomAD)
Structure: AlphaFold pLDDT 74.50 · 25 PDB
Residue 9: 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-leu9his (accessed [today's date]).

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