PTPN13

protein tyrosine phosphatase non-receptor type 13, the group of Protein tyrosine phosphatases non-receptor type|PDZ domain containing|FERM domain containing

Basic information

Region (hg38): 4:86594315-86815171

Links

ENSG00000163629 ∙ ∙ OMIM:600267 ∙ HGNC:9646 ∙ Uniprot:Q12923 ∙ 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 PTPN13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPN13 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				4	1	5
missense			131	10	5	146
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	131	14	6

Variants in PTPN13

This is a list of pathogenic ClinVar variants found in the PTPN13 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-86635277-G-A			Likely benign (Oct 01, 2022)
4-86635308-G-A		not specified	Uncertain significance (Aug 12, 2024)
4-86672467-A-G		not specified	Uncertain significance (Dec 19, 2023)
4-86672491-C-T		not specified	Uncertain significance (Jun 05, 2024)
4-86672517-C-G			Benign (Jan 30, 2018)
4-86672521-C-G		not specified	Likely benign (Mar 24, 2023)
4-86689023-C-A		not specified	Uncertain significance (Nov 12, 2021)
4-86689084-G-A		not specified	Uncertain significance (Nov 10, 2022)
4-86689149-G-A		not specified	Uncertain significance (Aug 10, 2021)
4-86689168-T-C		not specified	Uncertain significance (Jun 17, 2024)
4-86693587-A-G		not specified	Uncertain significance (Aug 21, 2023)
4-86693609-G-A		not specified	Uncertain significance (May 27, 2022)
4-86693612-A-C		not specified	Uncertain significance (Jan 24, 2024)
4-86693612-A-T		not specified	Uncertain significance (Sep 29, 2023)
4-86693642-G-A		not specified	Uncertain significance (Oct 13, 2021)
4-86693648-G-A		not specified	Uncertain significance (Mar 28, 2023)
4-86693654-G-A		not specified	Uncertain significance (Mar 21, 2023)
4-86701260-T-A		not specified	Uncertain significance (Sep 04, 2024)
4-86701267-G-C		not specified	Uncertain significance (Aug 30, 2021)
4-86701268-A-G		not specified	Uncertain significance (Mar 11, 2022)
4-86701282-C-T		not specified	Uncertain significance (Nov 17, 2022)
4-86701350-T-G		not specified	Uncertain significance (Oct 26, 2021)
4-86701400-G-A		not specified	Likely benign (Jun 22, 2023)
4-86701425-C-T			Benign (Feb 09, 2018)
4-86701432-C-G		not specified	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPN13	protein_coding	protein_coding	ENST00000436978	47	220857

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.42e-25	1.00	124574	0	115	124689	0.000461

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.576	1174	1.23e+3	0.954	0.0000619	16206
Missense in Polyphen		453	510.83	0.8868		6731
Synonymous	0.461	431	443	0.972	0.0000225	4743
Loss of Function	4.83	61	118	0.519	0.00000617	1570

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000902	0.000901
Ashkenazi Jewish	0.00	0.00
East Asian	0.000622	0.000612
Finnish	0.000466	0.000464
European (Non-Finnish)	0.000497	0.000487
Middle Eastern	0.000622	0.000612
South Asian	0.000268	0.000261
Other	0.000497	0.000495

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tyrosine phosphatase which regulates negatively FAS- induced apoptosis and NGFR-mediated pro-apoptotic signaling (PubMed:15611135). May regulate phosphoinositide 3-kinase (PI3K) signaling through dephosphorylation of PIK3R2 (PubMed:23604317). {ECO:0000269|PubMed:15611135, ECO:0000269|PubMed:23604317}.
• Pathway: Apoptosis - Homo sapiens (human);Apoptosis Modulation and Signaling;Ectoderm Differentiation;Metabolism of lipids;Metabolism;fas signaling pathway (cd95);Ephrin B reverse signaling;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism;Fc-epsilon receptor I signaling in mast cells (Consensus)

Recessive Scores

• pRec: 0.176

Intolerance Scores

• loftool: 0.839
• rvis_EVS: 1.3
• rvis_percentile_EVS: 93.89

Haploinsufficiency Scores

• pHI: 0.531
• hipred: Y
• hipred_score: 0.672
• ghis: 0.496

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.804

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptpn13
• Phenotype: cellular phenotype; growth/size/body region phenotype; hematopoietic system phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype

Gene ontology

• Biological process: protein dephosphorylation;phosphatidylinositol biosynthetic process;regulation of phosphatidylinositol 3-kinase signaling;peptidyl-tyrosine dephosphorylation;cellular response to cytokine stimulus
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytoskeleton;plasma membrane;lamellipodium;neuron projection;cell body;extracellular exosome
• Molecular function: protein tyrosine phosphatase activity;protein binding;phosphatidylinositol 3-kinase regulatory subunit binding