Is PPIP5K2 p.Ala313= (c.939C>T) pathogenic?

PPIP5K2 p.Ala313= (c.939C>T) is classified Likely benign in PPIP5K2 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-11-13). Absent from gnomAD v4.1.

How common is PPIP5K2 p.Ala313= (c.939C>T) in the general population?

PPIP5K2 p.Ala313= (c.939C>T) is absent from gnomAD v4.1 (gnomAD).

PPIP5K2 p.Ala313=

c.939C>T · VCV4971592

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 1	GERP 1.9, phastCons 1
Overall
CADD	13.11	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PPIP5K2
Protein: p.Ala313=
Coding: c.939C>T
MANE Select: NM_001276277
Type: single nucleotide variant
Location: chr5:103151285 (GRCh38)
Gene constraint: LOEUF 0.973 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.73 · 21 PDB
Residue 313: a β-strand

Full PPIP5K2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PPIP5K2 p.Ala1162Thr Uncertain significance ★ ⚠ same type
PPIP5K2 p.Ala1168Thr Uncertain significance ★ ⚠ same type
PPIP5K2 p.Ala1207Val Uncertain significance ★ ⚠ same type
PPIP5K2 p.Ala28Val Uncertain significance ★ ⚠ same type
PPIP5K2 p.Ala300Gly Uncertain significance ★ ⚠ same type
PPIP5K2 p.Arg1001His Uncertain significance ★ ⚠ same type
PPIP5K2 p.Arg1002Gln Uncertain significance ★ ⚠ same type
PPIP5K2 p.Arg1005Lys 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/ppip5k2-p-ala313 (accessed [today's date]).

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