PTPN21

protein tyrosine phosphatase non-receptor type 21, the group of Protein tyrosine phosphatases non-receptor type|FERM domain containing

Basic information

Region (hg38): 14:88465778-88555007

Links

ENSG00000070778 ∙ NCBI:11099 ∙ OMIM:603271 ∙ HGNC:9651 ∙ Uniprot:Q16825 ∙ 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 PTPN21 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPN21 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				1	1	2
missense			72	2	2	76
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	72	3	3

Variants in PTPN21

This is a list of pathogenic ClinVar variants found in the PTPN21 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-88468175-C-T		not specified	Uncertain significance (May 03, 2023)
14-88468232-T-C		not specified	Uncertain significance (Sep 07, 2022)
14-88468259-C-G		not specified	Uncertain significance (Jul 19, 2023)
14-88468945-T-G		not specified	Uncertain significance (Apr 04, 2024)
14-88469010-T-C		not specified	Uncertain significance (Oct 27, 2023)
14-88469013-G-A		not specified	Uncertain significance (Jul 20, 2021)
14-88469016-C-T			Benign (Apr 04, 2018)
14-88469040-G-A		not specified	Uncertain significance (May 15, 2024)
14-88469044-G-A		not specified	Uncertain significance (Dec 16, 2021)
14-88469683-C-T			Likely benign (Feb 01, 2023)
14-88469730-C-T		not specified	Uncertain significance (Oct 27, 2023)
14-88472288-T-C		not specified	Uncertain significance (Oct 12, 2022)
14-88472338-C-T		not specified	Uncertain significance (Jun 29, 2023)
14-88472374-G-A		not specified	Uncertain significance (Jun 24, 2022)
14-88472379-C-G		not specified	Uncertain significance (Nov 09, 2023)
14-88472396-G-C		not specified	Uncertain significance (Jul 25, 2023)
14-88472437-T-C		not specified	Uncertain significance (Sep 17, 2021)
14-88473673-C-T		not specified	Uncertain significance (Feb 05, 2024)
14-88473703-C-T		not specified	Uncertain significance (Nov 05, 2021)
14-88473723-C-T		not specified	Uncertain significance (Aug 26, 2022)
14-88478950-C-G		not specified	Uncertain significance (May 16, 2024)
14-88479005-G-C		not specified	Uncertain significance (Jan 29, 2024)
14-88479011-T-C		not specified	Uncertain significance (Dec 14, 2021)
14-88479045-T-G		not specified	Uncertain significance (Nov 21, 2022)
14-88479075-G-C			Likely benign (Apr 04, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPN21	protein_coding	protein_coding	ENST00000556564	18	88956

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.21e-12	1.00	125655	0	93	125748	0.000370

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.513	685	724	0.946	0.0000465	7602
Missense in Polyphen		221	284.64	0.77641		3106
Synonymous	-0.778	329	312	1.06	0.0000223	2313
Loss of Function	3.77	30	62.1	0.483	0.00000362	644

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000602	0.000598
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000452	0.000435
Finnish	0.0000932	0.0000462
European (Non-Finnish)	0.000406	0.000378
Middle Eastern	0.000452	0.000435
South Asian	0.000799	0.000784
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Signaling events mediated by focal adhesion kinase (Consensus)

Recessive Scores

• pRec: 0.146

Intolerance Scores

• loftool: 0.438
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.36

Haploinsufficiency Scores

• pHI: 0.158
• hipred: Y
• hipred_score: 0.747
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.637

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptpn21

Zebrafish Information Network

• Gene name: ptpn21
• Affected structure: melanocyte
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: protein dephosphorylation;peptidyl-tyrosine dephosphorylation
• Cellular component: cytoplasm;cytoskeleton
• Molecular function: protein tyrosine phosphatase activity;protein binding