Is PI4KB p.Val37= (c.111C>T) pathogenic?

PI4KB p.Val37= (c.111C>T) is classified Likely benign in PI4KB (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-16). Very rare (popmax 0.00223%, eas).

How common is PI4KB p.Val37= (c.111C>T) in the general population?

PI4KB p.Val37= (c.111C>T) is very rare (popmax 0.00223%, eas) (gnomAD).

PI4KB p.Val37=

c.111C>T · VCV3888601

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

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 -0.034	GERP -5.2, phastCons 0.18
Overall
CADD	5.258	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,840 alleles

Filtering AF 0.000124% ClinGen BA1/BS1 input FAF95, joint · FAF99 9e-05%

Overall 0.000435% 7/1,608,750 alleles · very rare exomes 7/1,456,502 · genomes 0/152,248 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,840
Remaining individualsnot grpmax-eligible	0.00161%	62,274
European (non-Finnish)	0.000425%	235,463

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: PI4KB
Protein: p.Val37=
Coding: c.111C>T
MANE Select: NM_001369623
Type: single nucleotide variant
Location: chr1:151316371 (GRCh38)
Gene constraint: LOEUF 0.421 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 72.97 · 20 PDB
Residue 37: the pik helical domain

Full PI4KB gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PI4KB p.Val37Ile Uncertain significance ★ ⚠ same residue
PI4KB p.Ile312Val Uncertain significance ★★ ⚠ same type
PI4KB p.Tyr175Cys Uncertain significance ★★ ⚠ same type
PI4KB c.-17G>A Uncertain significance ★ same type
PI4KB c.-6G>T Uncertain significance ★ same type
PI4KB p.Ala106Val Uncertain significance ★ ⚠ same type
PI4KB p.Ala605Gly Uncertain significance ★ ⚠ same type
PI4KB p.Ala67Val 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/pi4kb-p-val37 (accessed [today's date]).

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