Is CSNK2A2 p.Arg245Ser (c.733C>A) pathogenic?

CSNK2A2 p.Arg245Ser (c.733C>A) is classified Uncertain significance in CSNK2A2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-29). AlphaMissense: likely pathogenic (0.9521); Absent from gnomAD v4.1.

How common is CSNK2A2 p.Arg245Ser (c.733C>A) in the general population?

CSNK2A2 p.Arg245Ser (c.733C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CSNK2A2 p.Arg245Ser (c.733C>A)?

AlphaMissense predicts likely pathogenic (score 0.9521) — an in-silico prediction, not a clinical call.

CSNK2A2 p.Arg245Ser

c.733C>A · VCV3497844

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9521 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,612,210)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.9521	likely pathogenic
REVEL	0.444	indeterminate
SaProt	LLR -13.02	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.7	GERP 2.6, phastCons 1
Regional constraint	o/e 0.60	unconstrained · MANE · 2,609 bp · p 3.3e-06 · regional, not allelic
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

No allele count reported in gnomAD v4.1 (AN 1,612,210). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CSNK2A2
Protein: p.Arg245Ser
Coding: c.733C>A
MANE Select: NM_001896
Type: single nucleotide variant
Location: chr16:58166678 (GRCh38)
Gene constraint: LOEUF 0.424 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 94.91 · 59 PDB
Residue 245: the protein kinase domain; an α-helix

Full CSNK2A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CSNK2A2 c.104+271G>A Benign ★★ same type
CSNK2A2 c.104+50C>T Benign ★★ same type
CSNK2A2 c.369+188A>G Benign ★★ same type
CSNK2A2 c.370-122A>G Benign ★★ same type
CSNK2A2 c.514-60T>C Benign ★★ same type
CSNK2A2 c.727-29T>G Benign ★★ same type
CSNK2A2 c.828-140C>A Benign ★★ same type
CSNK2A2 c.828-58G>A Benign ★★ 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/csnk2a2-p-arg245ser (accessed [today's date]).

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