PTPRM

protein tyrosine phosphatase receptor type M, the group of Fibronectin type III domain containing|I-set domain containing|Protein tyrosine phosphatases receptor type|Ig-like cell adhesion molecule family

Basic information

Region (hg38): 18:7566781-8406861

Previous symbols: [ "PTPRL1" ]

Links

ENSG00000173482 ∙ NCBI:5797 ∙ OMIM:176888 ∙ HGNC:9675 ∙ Uniprot:P28827 ∙ 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 PTPRM gene.

• Inborn genetic diseases (36 variants)
• not provided (6 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRM 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					4	4
missense			37		2	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	37	0	7

Variants in PTPRM

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

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

Position	Type	Phenotype	Significance	ClinVar
18-7774150-T-C		PTPRM-related disorder	Likely benign (Feb 20, 2019)
18-7774173-A-G		not specified	Uncertain significance (Feb 17, 2022)
18-7774192-T-A		PTPRM-related disorder	Benign (Feb 17, 2020)
18-7774210-C-T			Benign (Oct 09, 2018)
18-7774215-A-G		not specified	Uncertain significance (Aug 17, 2022)
18-7774222-G-A		PTPRM-related disorder	Likely benign (Apr 11, 2019)
18-7774241-A-G		not specified	Uncertain significance (Jan 26, 2022)
18-7888117-C-A		not specified	Uncertain significance (Jul 09, 2021)
18-7888232-A-G		not specified	Uncertain significance (Jul 05, 2023)
18-7888286-G-A		not specified	Uncertain significance (Dec 16, 2022)
18-7888308-T-C		PTPRM-related disorder	Likely benign (Mar 08, 2019)
18-7888316-C-A		not specified	Uncertain significance (Nov 21, 2023)
18-7888331-A-G		not specified	Uncertain significance (Oct 03, 2022)
18-7906539-G-C		not specified	Uncertain significance (Dec 15, 2023)
18-7906550-A-G		not specified	Uncertain significance (Jul 06, 2022)
18-7906562-A-C		not specified	Uncertain significance (May 24, 2023)
18-7926614-T-C		PTPRM-related disorder	Likely benign (May 21, 2019)
18-7949172-T-C		PTPRM-related disorder	Benign/Likely benign (Aug 09, 2019)
18-7949277-G-A		not specified	Uncertain significance (Dec 19, 2023)
18-7949292-C-T		not specified	Uncertain significance (Feb 12, 2024)
18-7955114-C-G		PTPRM-related disorder	Likely benign (Jul 30, 2019)
18-7955128-C-T		PTPRM-related disorder	Likely benign (Jul 10, 2019)
18-7955153-G-A		not specified	Uncertain significance (Aug 13, 2021)
18-7955281-C-T			Benign (Jul 16, 2018)
18-7955289-C-G		not specified	Uncertain significance (Nov 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPRM	protein_coding	protein_coding	ENST00000580170	33	840080

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000198	125667	0	81	125748	0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.84	616	849	0.725	0.0000478	9613
Missense in Polyphen		169	333.59	0.50661		3788
Synonymous	-0.566	330	317	1.04	0.0000189	2809
Loss of Function	7.25	12	83.4	0.144	0.00000463	918

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.00536	0.00537
East Asian	0.0000544	0.0000544
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000114	0.000114
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000981	0.0000980
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in cell-cell adhesion through homophilic interactions. May play a key role in signal transduction and growth control. {ECO:0000269|PubMed:16456543}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Adherens junction - Homo sapiens (human);Nectin adhesion pathway (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.421
• rvis_EVS: -2.03
• rvis_percentile_EVS: 1.7

Haploinsufficiency Scores

• pHI: 0.206
• hipred: Y
• hipred_score: 0.708
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.617

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptprm
• Phenotype: 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); muscle phenotype

Gene ontology

• Biological process: negative regulation of endothelial cell proliferation;protein dephosphorylation;homophilic cell adhesion via plasma membrane adhesion molecules;signal transduction;negative regulation of endothelial cell migration;retina layer formation;negative regulation of angiogenesis;neuron projection development;retinal ganglion cell axon guidance;peptidyl-tyrosine dephosphorylation;response to drug;positive regulation of blood vessel diameter
• Cellular component: cytoplasm;plasma membrane;integral component of plasma membrane;cell-cell junction;cell-cell adherens junction;lamellipodium;perinuclear region of cytoplasm
• Molecular function: protein tyrosine phosphatase activity;transmembrane receptor protein tyrosine phosphatase activity;protein binding;identical protein binding;cadherin binding