PPP1R13B

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

Basic information

Region (hg38): 14:103733194-103847575

Links

ENSG00000088808 ∙ NCBI:23368 ∙ OMIM:606455 ∙ HGNC:14950 ∙ Uniprot:Q96KQ4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PPP1R13B gene.

• Inborn genetic diseases (44 variants)
• not provided (10 variants)
• Childhood-onset schizophrenia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1R13B gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	5	7
missense			42	3	3	48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	5	8

Variants in PPP1R13B

This is a list of pathogenic ClinVar variants found in the PPP1R13B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
14-103735173-C-T		not specified	Uncertain significance (Mar 04, 2024)
14-103736034-C-T		not specified	Uncertain significance (Dec 13, 2023)
14-103736036-G-T		not specified	Uncertain significance (Aug 12, 2021)
14-103736082-C-T		not specified	Uncertain significance (Nov 06, 2023)
14-103736092-T-C		not specified	Uncertain significance (Jan 23, 2023)
14-103736111-G-A			Likely benign (Dec 01, 2022)
14-103737780-G-A		not specified	Uncertain significance (Jul 16, 2021)
14-103737845-G-A			Benign (Jul 17, 2018)
14-103738703-A-G		not specified	Uncertain significance (Sep 14, 2022)
14-103738737-T-C		not specified	Uncertain significance (Oct 30, 2023)
14-103738752-C-T		not specified	Uncertain significance (Feb 27, 2024)
14-103738753-G-A			Benign (Jul 23, 2018)
14-103738758-C-T		not specified	Uncertain significance (Jul 21, 2021)
14-103738950-A-G		not specified	Uncertain significance (Oct 17, 2023)
14-103738975-C-T		not specified	Uncertain significance (Oct 12, 2021)
14-103739017-G-A		not specified	Uncertain significance (Aug 10, 2021)
14-103739020-T-C		not specified	Uncertain significance (Dec 22, 2023)
14-103739885-C-T			Benign (Jul 23, 2018)
14-103739894-G-A		not specified	Uncertain significance (Jun 02, 2023)
14-103739895-G-A		not specified	Uncertain significance (Feb 05, 2024)
14-103739919-T-A		not specified	Uncertain significance (Oct 02, 2023)
14-103739920-C-G		not specified	Uncertain significance (Sep 20, 2023)
14-103739927-G-A		not specified	Uncertain significance (Mar 28, 2023)
14-103739969-G-A		not specified	Uncertain significance (Aug 12, 2021)
14-103739988-T-C		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP1R13B	protein_coding	protein_coding	ENST00000202556	17	113839

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00189	124794	0	11	124805	0.0000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.53	553	664	0.833	0.0000411	7062
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000292	0.0000292
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000556
Finnish	0.000141	0.000139
European (Non-Finnish)	0.0000442	0.0000441
Middle Eastern	0.0000557	0.0000556
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;TP53 Regulates Transcription of Cell Death Genes;RNA Polymerase II Transcription;Activation of PUMA and translocation to mitochondria;Activation of BH3-only proteins;Intrinsic Pathway for Apoptosis;Apoptosis;Programmed Cell Death;TP53 Regulates Transcription of Genes Involved in Cytochrome C Release;TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain;Regulation of TP53 Activity through Association with Co-factors;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Direct p53 effectors;TP53 Regulates Transcription of Death Receptors and Ligands (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.201
• rvis_EVS: -1.79
• rvis_percentile_EVS: 2.24

Haploinsufficiency Scores

• pHI: 0.159
• hipred: Y
• hipred_score: 0.800
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.608

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp1r13b
• Phenotype: homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; immune system phenotype; normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• 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
• Cellular component: nucleus;nucleoplasm;cytoplasm;mitochondrion;cytosol;plasma membrane
• Molecular function: p53 binding;protein binding;transcription factor binding