PTPRG

protein tyrosine phosphatase receptor type G, the group of Fibronectin type III domain containing|Protein tyrosine phosphatases receptor type

Basic information

Region (hg38): 3:61561568-62297609

Previous symbols: [ "PTPG" ]

Links

ENSG00000144724 ∙ NCBI:5793 ∙ OMIM:176886 ∙ HGNC:9671 ∙ Uniprot:P23470 ∙ 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 PTPRG gene.

• Inborn genetic diseases (68 variants)
• not provided (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRG 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				8	3	11
missense			66	2	1	69
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				6		6
Total	0	0	66	16	4

Variants in PTPRG

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

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

Position	Type	Phenotype	Significance	ClinVar
3-61562292-G-A		not specified	Uncertain significance (Jun 27, 2022)
3-61562313-G-C		not specified	Uncertain significance (Nov 22, 2022)
3-61562327-C-T			Benign (Nov 20, 2018)
3-61562336-A-G		not specified	Uncertain significance (Feb 14, 2024)
3-61562345-G-C		not specified	Uncertain significance (Sep 25, 2023)
3-61562358-T-C		not specified	Uncertain significance (Mar 23, 2023)
3-61748878-C-T		not specified	Uncertain significance (Dec 19, 2022)
3-61748915-T-A		not specified	Uncertain significance (May 22, 2023)
3-61748928-G-A		not specified	Uncertain significance (Jan 29, 2024)
3-61748961-G-A		not specified	Uncertain significance (Dec 27, 2023)
3-61748966-G-A			Benign (Dec 31, 2019)
3-61989631-A-C		not specified	Uncertain significance (Jan 04, 2024)
3-61989717-G-T		not specified	Uncertain significance (Aug 23, 2021)
3-61989748-A-T		not specified	Uncertain significance (Feb 02, 2022)
3-61989759-A-G		not specified	Uncertain significance (Jul 25, 2023)
3-62003354-A-G		not specified	Uncertain significance (Oct 21, 2021)
3-62003406-T-A		not specified	Uncertain significance (Nov 18, 2022)
3-62003445-A-G		not specified	Uncertain significance (Dec 16, 2023)
3-62003448-G-T		not specified	Uncertain significance (Nov 28, 2023)
3-62003471-A-G		not specified	Uncertain significance (Feb 03, 2022)
3-62003475-A-G		not specified	Uncertain significance (Jul 09, 2021)
3-62078214-A-G		not specified	Uncertain significance (Jan 11, 2023)
3-62132606-G-C		not specified	Uncertain significance (Dec 11, 2023)
3-62132645-G-C		not specified	Uncertain significance (Jul 06, 2021)
3-62157158-A-G			Likely benign (Dec 05, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPRG	protein_coding	protein_coding	ENST00000474889	30	736046

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000507	1.00	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.230	833	852	0.978	0.0000488	9544
Missense in Polyphen		262	328.06	0.79863		3988
Synonymous	-1.07	348	324	1.08	0.0000213	2718
Loss of Function	5.44	24	74.8	0.321	0.00000393	864

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000366	0.000365
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000130	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000251	0.000246
Middle Eastern	0.000130	0.000109
South Asian	0.000168	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possesses tyrosine phosphatase activity. {ECO:0000269|PubMed:19167335}.

Recessive Scores

• pRec: 0.183

Intolerance Scores

• loftool: 0.417
• rvis_EVS: -1.74
• rvis_percentile_EVS: 2.43

Haploinsufficiency Scores

• pHI: 0.728
• hipred: N
• hipred_score: 0.492
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.869

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptprg
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: transmembrane receptor protein tyrosine kinase signaling pathway;brain development;negative regulation of epithelial cell migration;negative regulation of neuron projection development;peptidyl-tyrosine dephosphorylation;regulation of homophilic cell adhesion
• Cellular component: integral component of plasma membrane;extracellular exosome
• Molecular function: protein tyrosine phosphatase activity;transmembrane receptor protein tyrosine phosphatase activity;protein binding;identical protein binding