PTPN18

protein tyrosine phosphatase non-receptor type 18, the group of Protein tyrosine phosphatases non-receptor type

Basic information

Region (hg38): 2:130356044-130375405

Links

ENSG00000072135 ∙ NCBI:26469 ∙ OMIM:606587 ∙ HGNC:9649 ∙ Uniprot:Q99952 ∙ 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 PTPN18 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPN18 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			47			47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	0	0

Variants in PTPN18

This is a list of pathogenic ClinVar variants found in the PTPN18 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-130356114-C-T		not specified	Uncertain significance (Jan 08, 2024)
2-130356159-C-T		not specified	Uncertain significance (Sep 14, 2022)
2-130356160-G-A		not specified	Uncertain significance (Oct 20, 2023)
2-130356160-G-T		not specified	Uncertain significance (Aug 12, 2021)
2-130358906-G-C		not specified	Uncertain significance (Jun 13, 2024)
2-130358924-G-A		not specified	Uncertain significance (Nov 20, 2023)
2-130358931-G-A		not specified	Uncertain significance (Jun 11, 2021)
2-130358958-A-G		not specified	Uncertain significance (Mar 21, 2022)
2-130358963-G-C		not specified	Uncertain significance (Oct 22, 2021)
2-130359286-T-C		not specified	Uncertain significance (Jan 04, 2024)
2-130359308-G-C		not specified	Uncertain significance (Jun 17, 2024)
2-130359459-C-G		not specified	Uncertain significance (Jun 24, 2022)
2-130359482-T-G		not specified	Uncertain significance (Dec 16, 2023)
2-130359645-G-A		not specified	Uncertain significance (Mar 14, 2023)
2-130369145-C-T		not specified	Uncertain significance (Aug 30, 2021)
2-130369146-G-A		not specified	Uncertain significance (May 24, 2024)
2-130369160-G-C		not specified	Uncertain significance (Aug 17, 2022)
2-130369173-T-G		not specified	Uncertain significance (Feb 17, 2024)
2-130369777-T-C		not specified	Uncertain significance (Oct 06, 2022)
2-130369793-T-G		not specified	Uncertain significance (Jun 29, 2022)
2-130370094-G-A		not specified	Uncertain significance (Dec 20, 2023)
2-130370123-C-T		not specified	Uncertain significance (Aug 30, 2021)
2-130370131-G-A		not specified	Uncertain significance (Aug 11, 2022)
2-130370133-T-G		not specified	Uncertain significance (Oct 27, 2022)
2-130370162-G-C		not specified	Uncertain significance (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPN18	protein_coding	protein_coding	ENST00000175756	15	19403

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.50e-9	0.821	125632	0	116	125748	0.000461

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.332	241	256	0.942	0.0000160	2934
Missense in Polyphen		85	94.173	0.90259		1040
Synonymous	0.497	96	102	0.937	0.00000644	928
Loss of Function	1.62	18	27.1	0.664	0.00000141	298

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000924	0.000924
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000167	0.000167
Middle Eastern	0.0000544	0.0000544
South Asian	0.00206	0.00206
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Differentially dephosphorylate autophosphorylated tyrosine kinases which are known to be overexpressed in tumor tissues.
• Pathway: B Cell Receptor Signaling Pathway;Signal Transduction;Fibroblast growth factor-1;BCR;Downregulation of ERBB2 signaling;EGFR1;Signaling by ERBB2;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.414
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.43

Haploinsufficiency Scores

• pHI: 0.0761
• hipred: N
• hipred_score: 0.280
• ghis: 0.488

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0457

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptpn18

Gene ontology

• Biological process: blastocyst formation;protein dephosphorylation;peptidyl-tyrosine dephosphorylation;ERBB2 signaling pathway;cellular response to cytokine stimulus;negative regulation of ERBB signaling pathway
• Cellular component: nucleoplasm;cytosol
• Molecular function: protein tyrosine phosphatase activity;non-membrane spanning protein tyrosine phosphatase activity;protein binding