Is CSNK2B p.Ser11Phe (c.32C>T) pathogenic?

CSNK2B p.Ser11Phe (c.32C>T) is classified Uncertain significance in CSNK2B (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-07). AlphaMissense: likely pathogenic (0.9412); Absent from gnomAD v4.1.

How common is CSNK2B p.Ser11Phe (c.32C>T) in the general population?

CSNK2B p.Ser11Phe (c.32C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CSNK2B p.Ser11Phe (c.32C>T)?

AlphaMissense predicts likely pathogenic (score 0.9412) — an in-silico prediction, not a clinical call.

CSNK2B p.Ser11Phe

c.32C>T · rs2536947688 · VCV1803327

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9412 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.9412	likely pathogenic
REVEL	0.344	indeterminate
SaProt	LLR -15.64	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 7.6	GERP 0.8, phastCons 1
Regional constraint	o/e 0.39	unconstrained · MANE · 3,091 bp · p 1.2e-24 · regional, not allelic
Overall
CADD	33.0	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

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: CSNK2B
Protein: p.Ser11Phe
Coding: c.32C>T
MANE Select: NM_001320
dbSNP: rs2536947688
Type: single nucleotide variant
Location: chr6:31666863 (GRCh38)
Gene constraint: LOEUF 0.237 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 93.70 · 10 PDB
Residue 11: a UniProt-annotated variant site (in pobinds; associated in cis with c-86); an α-helix

Full CSNK2B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CSNK2B c.175+1G>A Pathogenic/Likely pathogenic ★★ same type
CSNK2B c.291+1G>A Pathogenic/Likely pathogenic ★★ same type
CSNK2B c.291+1G>T Likely pathogenic ★★ same type
CSNK2B c.292-2A>C Pathogenic/Likely pathogenic ★★ same type
CSNK2B c.292-2A>G Pathogenic/Likely pathogenic ★★ same type
CSNK2B c.292-2A>T Pathogenic/Likely pathogenic ★★ same type
CSNK2B c.367+1G>C Pathogenic ★★ same type
CSNK2B c.557+1G>C Pathogenic/Likely pathogenic ★★ 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/csnk2b-p-ser11phe (accessed [today's date]).

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