PTPN20

protein-coding

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

Gene summary

The product of this gene belongs to the family of classical tyrosine-specific protein tyrosine phosphatases. Many protein tyrosine phosphatases have been shown to regulate fundamental cellular processes. The encoded protein appears to be targeted to sites of actin polymerization. A pseudogene of this gene has been defined on chromosome 10. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2014]

Previous symbols:

PTPN20A
PTPN20B

MANE transcript

NM_001042357.5

Inheritance

—

ClinVar variants

U:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.59

Max pathogenic AF

—

Genomic locus

chr10:46,911,396-47,002,488

External References & Databases

Ensembl (ENSG00000204179)

Transcript & Mutation Effects

hg38 • Region Span ~91.1 kb

Loading mutation effect viewer...

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 PTPN20 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001042357.5. 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						0
missense			1 clinvar			1
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	1	0	0	1

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 149 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001042357.5	RefSeq	NP_001035816.1	10	MANE Select
ENST00000374339.5	Ensembl	ENSP00000363459.3	10	MANE Select
NM_001042358.5	RefSeq	NP_001035817.1	10	Standard
NM_001042359.4	RefSeq	NP_001035818.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

peptidyl-tyrosine dephosphorylation
cellular response to cytokine stimulus

Molecular Function

protein tyrosine phosphatase activity

Cellular Component

nucleoplasm
cytoplasm
microtubule organizing center
microtubule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374339
Coding exons: 10
Length: 91091
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.554	4	8.56	0.467	3.61e-7	2786
Missense (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

Population LoF Frequency

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

dbNSFP Gene Annotations

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

Essentials

Essential (gene trap): N