PTPN20

protein tyrosine phosphatase non-receptor type 20, the group of Protein tyrosine phosphatases non-receptor type

Basic information

Region (hg38): 10:46911396-47002488

Previous symbols: [ "PTPN20A", "PTPN20B" ]

Links

ENSG00000204179 ∙ NCBI:26095 ∙ OMIM:610630 ∙ HGNC:23423 ∙ Uniprot:Q4JDL3 ∙ 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 PTPN20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPN20 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						0
missense			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in PTPN20

This is a list of pathogenic ClinVar variants found in the PTPN20 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-46946636-G-A		not specified	Uncertain significance (Jun 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPN20	protein_coding	protein_coding	ENST00000374339	10	91091

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0159	0.482	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.554	4	8.56	0.467	3.61e-7	2786
Missense in Polyphen		0	0.34577	0		1006
Synonymous	1.04	1	3.48	0.288	1.94e-7	748
Loss of Function	-0.615	2	1.26	1.59	5.22e-8	276

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tyrosine-protein phosphatase targeted to sites of actin polymerization in response of varied extracellular stimuli. Has tyrosine phosphatase activity towards various tyrosyl phosphorylated substrates.

Recessive Scores

• pRec: 0.0831

Haploinsufficiency Scores

• pHI: 0.545
• ghis: 0.397

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Ptpn20
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: peptidyl-tyrosine dephosphorylation;cellular response to cytokine stimulus
• Cellular component: nucleoplasm;cytoplasm;microtubule organizing center;microtubule
• Molecular function: protein tyrosine phosphatase activity