PPP1R13L

protein phosphatase 1 regulatory subunit 13 like, the group of Ankyrin repeat domain containing

Basic information

Region (hg38): 19:45379637-45406349

Links

ENSG00000104881 ∙ NCBI:10848 ∙ OMIM:607463 ∙ HGNC:18838 ∙ Uniprot:Q8WUF5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cardiomyopathy, arrhythmogenic, with or without ectodermal abnormalities	AR	Cardiovascular	The condition involves severe, early-onset dilated cardiomyopathy, and awareness may enable medical management; Cardiac transplant has been described	Cardiovascular; Craniofacial; Dental; Dermatologic	28069640; 32666529; 35924320; 35933355

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PPP1R13L gene.

• Inborn genetic diseases (38 variants)
• not provided (15 variants)
• Primary dilated cardiomyopathy (6 variants)
• Arrhythmogenic cardiomyopathy with variable ectodermal abnormalities (5 variants)
• PPP1R13L-associated cardiac phenotype (1 variants)
• OMIM:607463 (1 variants)
• Primary dilated cardiomyopathy;Orofacial cleft (1 variants)
• Multiple congenital anomalies/dysmorphic syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1R13L 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				3	3	6
missense			39			39
nonsense	1	1	1			3
start loss						0
frameshift	1	3				4
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			1		7	8
Total	2	4	41	3	10

Highest pathogenic variant AF is 0.0000131

Variants in PPP1R13L

This is a list of pathogenic ClinVar variants found in the PPP1R13L region.

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

Position	Type	Phenotype	Significance	ClinVar
19-45380010-A-G			Benign (May 24, 2021)
19-45380190-CT-GA		Primary dilated cardiomyopathy • Arrhythmogenic cardiomyopathy with variable ectodermal abnormalities	Likely pathogenic (Jun 10, 2020)
19-45380194-A-G		Inborn genetic diseases	Uncertain significance (Sep 14, 2021)
19-45380223-G-T		Inborn genetic diseases	Uncertain significance (Jun 12, 2023)
19-45380296-C-T			Benign (May 15, 2021)
19-45381801-G-A		PPP1R13L-associated cardiac phenotype	Uncertain significance (Jun 23, 2021)
19-45382459-T-C			Benign (May 24, 2021)
19-45382562-C-T		Inborn genetic diseases	Uncertain significance (Dec 20, 2023)
19-45382579-C-G		Primary dilated cardiomyopathy	Uncertain significance (Jun 10, 2020)
19-45382597-G-T		Inborn genetic diseases	Uncertain significance (Jul 19, 2023)
19-45382610-G-A		Inborn genetic diseases	Uncertain significance (Nov 07, 2023)
19-45382649-C-A			Uncertain significance (Jul 01, 2022)
19-45382656-G-A			Likely benign (Jul 01, 2022)
19-45382721-C-T		Inborn genetic diseases	Uncertain significance (Jan 03, 2022)
19-45385569-G-C		Cardio-cutaneous syndrome • Arrhythmogenic cardiomyopathy with variable ectodermal abnormalities	Pathogenic (Sep 26, 2023)
19-45385643-T-G		Primary dilated cardiomyopathy	Uncertain significance (Jun 10, 2020)
19-45385704-C-T			Benign (Apr 05, 2018)
19-45385837-C-T		Inborn genetic diseases	Uncertain significance (Sep 22, 2023)
19-45385854-G-C		Inborn genetic diseases	Uncertain significance (Aug 12, 2021)
19-45385857-C-T		Inborn genetic diseases	Uncertain significance (Nov 15, 2021)
19-45385878-A-G		Inborn genetic diseases	Uncertain significance (Oct 27, 2021)
19-45385923-A-C		Inborn genetic diseases	Uncertain significance (Dec 21, 2023)
19-45385950-T-C		Inborn genetic diseases	Uncertain significance (May 23, 2023)
19-45386174-G-T		Inborn genetic diseases	Uncertain significance (Dec 01, 2022)
19-45391868-T-C			Benign (May 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP1R13L	protein_coding	protein_coding	ENST00000418234	12	26716

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0321	0.968	125724	0	16	125740	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	392	487	0.804	0.0000324	5179
Missense in Polyphen		94	105.77	0.88869		1093
Synonymous	0.993	214	233	0.917	0.0000181	1790
Loss of Function	3.78	9	32.1	0.280	0.00000156	338

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000207	0.000206
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000455	0.0000440
Middle Eastern	0.0000545	0.0000544
South Asian	0.000133	0.000131
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator that plays a central role in regulation of apoptosis and transcription via its interaction with NF-kappa-B and p53/TP53 proteins. Blocks transcription of HIV-1 virus by inhibiting the action of both NF-kappa-B and SP1. Also inhibits p53/TP53 function, possibly by preventing the association between p53/TP53 and ASPP1 or ASPP2, and therefore suppressing the subsequent activation of apoptosis. {ECO:0000269|PubMed:10336463, ECO:0000269|PubMed:12134007, ECO:0000269|PubMed:12524540, ECO:0000269|PubMed:15489900}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Regulation of TP53 Activity through Association with Co-factors;Regulation of TP53 Activity;Transcriptional Regulation by TP53;TNFalpha;p53 pathway (Consensus)

Haploinsufficiency Scores

• pHI: 0.225
• hipred: Y
• hipred_score: 0.767
• ghis: 0.579

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.986

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp1r13l
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; endocrine/exocrine gland 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; vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system 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: negative regulation of transcription by RNA polymerase II;cardiac right ventricle morphogenesis;ventricular cardiac muscle tissue development;transcription, DNA-templated;apoptotic process;post-embryonic development;embryonic camera-type eye development;multicellular organism growth;hair cycle;positive regulation of cell differentiation;multicellular organismal homeostasis;cardiac muscle contraction;regulation of signal transduction by p53 class mediator
• Cellular component: nucleus;nucleoplasm;cytosol;cell junction;intercellular bridge
• Molecular function: transcription corepressor activity;protein binding;transcription factor binding;identical protein binding;cadherin binding