Is PI4KA p.Ser802= (c.2406C>T) pathogenic?

PI4KA p.Ser802= (c.2406C>T) is classified Conflicting classifications of pathogenicity in PI4KA (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2023-12-04). Ultra-rare (popmax 0.0133%, amr).

How common is PI4KA p.Ser802= (c.2406C>T) in the general population?

PI4KA p.Ser802= (c.2406C>T) is ultra-rare (popmax 0.0133%, amr) (gnomAD).

PI4KA p.Ser802=

c.2406C>T · rs150538650 · VCV2434705

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0133%, amr)

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 -10
Overall
CADD	0.1	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0133% Admixed American · 8/59,942 alleles

Filtering AF 0.00662% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00491%

Overall 0.00695% 112/1,610,392 alleles · ultra-rare exomes 109/1,458,282 · genomes 3/152,110 · joint denominator

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.0266%	3,765
Admixed Americangrpmax	0.0133%	7,493
South Asian	0.00659%	15,168
European (non-Finnish)	0.00654%	15,284
Remaining individualsnot grpmax-eligible	0.00481%	20,779
African / African-American	0.00134%	74,892

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: PI4KA
Protein: p.Ser802=
Coding: c.2406C>T
MANE Select: NM_058004
dbSNP: rs150538650
Type: single nucleotide variant
Location: chr22:20765616 (GRCh38)
Gene constraint: LOEUF 0.548 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.42 · 4 PDB
Residue 802: a UniProt-annotated variant site (in nedsplb); an α-helix

Full PI4KA gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PI4KA p.Arg618Ter Likely pathogenic ★★ same type
PI4KA p.Asp1854Asn Pathogenic/Likely pathogenic ★★ same type
PI4KA p.Glu1152Lys Likely pathogenic ★★ same type
PI4KA p.Pro1992Ser Likely pathogenic ★★ ⚠ same type
PI4KA p.Ala1037Thr Uncertain significance ★★ ⚠ same type
PI4KA p.Ala940Val Uncertain significance ★★ ⚠ same type
PI4KA p.Asp1713His Uncertain significance ★★ ⚠ same type
PI4KA p.Asp1866Asn 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/pi4ka-p-ser802 (accessed [today's date]).

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