Is PPP1CB p.Ser10= (c.30C>T) pathogenic?

PPP1CB p.Ser10= (c.30C>T) is classified Likely benign in PPP1CB (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-08-17). Very rare (popmax 0.00238%, sas); Associated with Cardiovascular phenotype.

What condition is associated with PPP1CB p.Ser10= (c.30C>T)?

PPP1CB p.Ser10= (c.30C>T) is associated with Cardiovascular phenotype (ClinVar).

How common is PPP1CB p.Ser10= (c.30C>T) in the general population?

PPP1CB p.Ser10= (c.30C>T) is very rare (popmax 0.00238%, sas) (gnomAD).

PPP1CB p.Ser10=

c.30C>T · rs1404169743 · VCV1727612

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00238%, sas)

Conditions

Cardiovascular phenotype

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 1.2	GERP -2.1, phastCons 1
Overall
CADD	13.35	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00238% South Asian · 2/84,032 alleles

Filtering AF 0.000395% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000163%

Overall 0.00071% 11/1,548,346 alleles · very rare exomes 10/1,396,240 · genomes 1/152,106 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00238%	42,016
Remaining individualsnot grpmax-eligible	0.00167%	59,968
African / African-American	0.00138%	72,492
European (non-Finnish)	0.000611%	163,645

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: PPP1CB
Protein: p.Ser10=
Coding: c.30C>T
MANE Select: NM_002709
dbSNP: rs1404169743
Type: single nucleotide variant
Location: chr2:28752154 (GRCh38)
Gene constraint: LOEUF 0.247 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 91.91

Full PPP1CB gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PPP1CB p.Ser10Asn Uncertain significance ★ ⚠ same residue
PPP1CB p.Ala2Val Uncertain significance ★★ ⚠ same condition
PPP1CB p.Leu11Val Uncertain significance ★★ ⚠ same condition
PPP1CB p.Leu6Val Uncertain significance ★★ ⚠ same condition
PPP1CB p.Phe234Leu Uncertain significance ★★ ⚠ same condition
PPP1CB p.Ser99Cys Uncertain significance ★★ ⚠ same condition
PPP1CB p.Ala127= Likely benign ★★ same condition
PPP1CB p.Ala228= Likely benign ★★ same condition

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/ppp1cb-p-ser10 (accessed [today's date]).

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