PPP1R13B

protein-coding

protein phosphatase 1 regulatory subunit 13B, the group of Ankyrin repeat domain containing|Protein phosphatase 1 regulatory subunits

Gene summary

This gene encodes a member of the ASPP (apoptosis-stimulating protein of p53) family of p53 interacting proteins. The protein contains four ankyrin repeats and an SH3 domain involved in protein-protein interactions. ASPP proteins are required for the induction of apoptosis by p53-family proteins. They promote DNA binding and transactivation of p53-family proteins on the promoters of proapoptotic genes. Expression of this gene is regulated by the E2F transcription factor. [provided by RefSeq, Jul 2008]

MANE transcript

NM_015316.3

Inheritance

—

ClinVar variants

U:169B:16

Top phenotype

Childhood-onset schizophrenia

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr14:103,733,195-103,847,575

External References & Databases

Ensembl (ENSG00000088808)

Transcript & Mutation Effects

hg38 • Region Span ~114.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PPP1R13B variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 163

not providedTotal: 13

Childhood-onset schizophreniaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015316.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	2 clinvar	5 clinvar	9
missense			164 clinvar	6 clinvar	3 clinvar	173
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	169	8	8	185

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015316.3	RefSeq	NP_056131.2	17	MANE Select
ENST00000202556.14	Ensembl	ENSP00000202556.9	17	MANE Select
ENST00000553739.2	Ensembl	ENSP00000450734.1	5	Standard
ENST00000555734.5	Ensembl	ENSP00000452376.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
Generic Transcription Pathway
TP53 Regulates Transcription of Cell Death Genes
RNA Polymerase II Transcription
Activation of PUMA and translocation to mitochondria

Biological Process

regulation of apoptotic process
negative regulation of cell cycle
intrinsic apoptotic signaling pathway by p53 class mediator
positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway
regulation of signal transduction by p53 class mediator

Molecular Function

p53 binding
protein binding
transcription factor binding

Cellular Component

nucleus
nucleoplasm
cytoplasm
mitochondrion
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000202556
Coding exons: 17
Length: 113839
Individuals with no LoFs: 124794
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 124805
p: 0.0000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.53	553	664	0.833	0.0000411	7062
Missense (PolyPhen)		149	237.05	0.62856		2490
Synonymous	0.289	270	276	0.978	0.0000192	2209
Loss of Function	5.77	8	53.6	0.149	0.00000277	581

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000056	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Regulator that plays a central role in regulation of apoptosis via its interaction with p53/TP53. Regulates TP53 by enhancing the DNA binding and transactivation function of TP53 on the promoters of proapoptotic genes in vivo. {ECO:0000269|PubMed:11684014}.;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.201
RVIS EVS: -1.79
RVIS percentile EVS: 2.24

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.608

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium