PTPN5

protein tyrosine phosphatase non-receptor type 5, the group of Protein tyrosine phosphatases non-receptor type

Basic information

Region (hg38): 11:18727927-18792721

Links

ENSG00000110786 ∙ NCBI:84867 ∙ OMIM:176879 ∙ HGNC:9657 ∙ Uniprot:P54829 ∙ 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 PTPN5 gene.

• Inborn genetic diseases (27 variants)
• not provided (16 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPN5 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			25	2		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	2	0

Variants in PTPN5

This is a list of pathogenic ClinVar variants found in the PTPN5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-18729473-C-T			not provided (-)
11-18729538-T-G		not specified	Uncertain significance (May 27, 2022)
11-18729668-C-T		not specified	Uncertain significance (Jul 12, 2023)
11-18729719-C-G		not specified	Uncertain significance (May 16, 2023)
11-18729722-G-A		not specified	Uncertain significance (Dec 02, 2022)
11-18729725-C-A		not specified	Uncertain significance (Sep 29, 2023)
11-18729810-A-T			not provided (-)
11-18729817-C-T			not provided (-)
11-18732600-A-G		not specified	Uncertain significance (Aug 13, 2021)
11-18732663-C-T		not specified	Uncertain significance (Oct 22, 2021)
11-18732668-G-A			not provided (-)
11-18732691-C-A		not specified	Uncertain significance (Jul 25, 2023)
11-18733237-C-T		not specified	Uncertain significance (Aug 16, 2021)
11-18733250-G-A			not provided (-)
11-18733257-G-T		not specified	Uncertain significance (Aug 30, 2021)
11-18733320-C-G		not specified	Uncertain significance (Dec 06, 2022)
11-18733323-A-G		not specified	Uncertain significance (Dec 19, 2022)
11-18733368-T-C			not provided (-)
11-18733591-G-A		not specified	Uncertain significance (Feb 27, 2023)
11-18737918-C-T		not specified	Uncertain significance (Mar 16, 2023)
11-18740652-T-C			not provided (-)
11-18740677-C-T		not specified	Uncertain significance (Dec 27, 2023)
11-18740692-C-T		not specified	Uncertain significance (May 04, 2023)
11-18740694-C-T		not specified	Uncertain significance (Oct 12, 2021)
11-18740710-G-A		not specified	Uncertain significance (Apr 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPN5	protein_coding	protein_coding	ENST00000358540	14	64794

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00142	0.999	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	294	353	0.833	0.0000220	3658
Missense in Polyphen		101	148.45	0.68038		1525
Synonymous	0.218	151	154	0.978	0.0000110	1117
Loss of Function	3.50	11	32.5	0.338	0.00000161	341

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.0000918	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.000197	0.000196
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate the activity of several effector molecules involved in synaptic plasticity and neuronal cell survival, including MAPKs, Src family kinases and NMDA receptors. {ECO:0000269|PubMed:21777200}.
• Pathway: MAPK signaling pathway - Homo sapiens (human);MAPK Signaling Pathway;EGF-EGFR Signaling Pathway (Consensus)

Recessive Scores

• pRec: 0.190

Intolerance Scores

• loftool: 0.498
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.14

Haploinsufficiency Scores

• pHI: 0.411
• hipred: Y
• hipred_score: 0.627
• ghis: 0.598

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.761

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptpn5
• 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; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); hematopoietic system phenotype

Gene ontology

• Biological process: protein dephosphorylation;peptidyl-tyrosine dephosphorylation;cellular response to cytokine stimulus
• Cellular component: nucleoplasm;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: phosphotyrosine residue binding;protein tyrosine phosphatase activity;protein binding