PTPRF

protein tyrosine phosphatase receptor type F, the group of Fibronectin type III domain containing|I-set domain containing|Protein tyrosine phosphatases receptor type

Basic information

Region (hg38): 1:43525187-43623666

Previous symbols: [ "LAR" ]

Links

ENSG00000142949 ∙ NCBI:5792 ∙ OMIM:179590 ∙ HGNC:9670 ∙ Uniprot:P10586 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• breasts and/or nipples, aplasia or hypoplasia of, 2 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Breasts and/or nipples, aplasia or hypoplasia of, 2	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic; Endocrine	24781087

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PTPRF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRF 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				28	11	39
missense			101	10	4	115
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				4	1	5
non coding				2	3	5
Total	0	0	101	40	18

Variants in PTPRF

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

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

Position	Type	Phenotype	Significance	ClinVar
1-43545104-C-G		not specified	Uncertain significance (Apr 06, 2024)
1-43545104-C-T		not specified	Uncertain significance (Jun 16, 2023)
1-43545130-G-A		not specified	Uncertain significance (Jul 05, 2023)
1-43545153-C-T			Likely benign (Jul 01, 2023)
1-43553493-C-G		not specified	Uncertain significance (Jan 31, 2023)
1-43553511-A-G		PTPRF-related disorder	Likely benign (Mar 21, 2019)
1-43553512-G-T		not specified	Uncertain significance (Jun 17, 2024)
1-43553599-A-C		not specified	Uncertain significance (Dec 19, 2022)
1-43553630-G-A		not specified	Uncertain significance (Mar 24, 2023)
1-43553634-C-T			Benign (Dec 31, 2019)
1-43553642-G-A			Benign (Dec 31, 2019)
1-43553813-A-G		not specified	Uncertain significance (Apr 20, 2024)
1-43553880-G-C		not specified	Uncertain significance (Jan 23, 2024)
1-43569658-C-T		not specified	Uncertain significance (Oct 04, 2024)
1-43569672-G-A		not specified	Uncertain significance (Oct 12, 2022)
1-43569681-C-T		PTPRF-related disorder	Benign (Oct 21, 2019)
1-43569710-C-A		not specified	Uncertain significance (Apr 12, 2022)
1-43569746-C-T		not specified	Uncertain significance (Jun 20, 2024)
1-43569773-G-A		not specified	Uncertain significance (Dec 20, 2023)
1-43578877-G-A		PTPRF-related disorder	Likely benign (May 20, 2019)
1-43578899-C-T		not specified	Uncertain significance (Jan 31, 2022)
1-43578904-G-A		PTPRF-related disorder	Benign (Jan 02, 2019)
1-43588737-G-A		not specified	Uncertain significance (May 13, 2024)
1-43588811-G-A		not specified	Uncertain significance (Dec 08, 2023)
1-43588836-A-G		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPRF	protein_coding	protein_coding	ENST00000359947	32	98486

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	4.68e-8	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.80	990	1.27e+3	0.779	0.0000882	12310
Missense in Polyphen		343	572.93	0.59868		5540
Synonymous	-0.596	555	537	1.03	0.0000401	3928
Loss of Function	7.86	10	90.8	0.110	0.00000458	955

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000329	0.000329
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000622	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possible cell adhesion receptor. It possesses an intrinsic protein tyrosine phosphatase activity (PTPase) and dephosphorylates EPHA2 regulating its activity.
• Disease: DISEASE: Aplasia or hypoplasia of the breasts and/or nipples 2 (BNAH2) [MIM:616001]: A group of congenital deformities encompassing total absence of breasts and nipple (amastia), absence of the nipple (athelia), and absence of the mammary gland (amazia). {ECO:0000269|PubMed:24781087}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Adherens junction - Homo sapiens (human);Insulin resistance - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;Insulin Signaling;Neuronal System;Synaptic adhesion-like molecules;EGFR1;Receptor-type tyrosine-protein phosphatases;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.330
• rvis_EVS: -3.92
• rvis_percentile_EVS: 0.2

Haploinsufficiency Scores

• pHI: 0.309
• hipred: Y
• hipred_score: 0.793
• ghis: 0.575

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.977

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptprf
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; 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); craniofacial phenotype; skeleton phenotype; cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); vision/eye phenotype; digestive/alimentary 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); renal/urinary system phenotype

Zebrafish Information Network

• Gene name: ptprfb
• Affected structure: Rohon-Beard neuron
• Phenotype tag: abnormal
• Phenotype quality: subdermal

Gene ontology

• Biological process: cell adhesion;transmembrane receptor protein tyrosine phosphatase signaling pathway;cell migration;neuron projection regeneration;peptidyl-tyrosine dephosphorylation;regulation of axon regeneration;synaptic membrane adhesion;negative regulation of receptor binding
• Cellular component: plasma membrane;integral component of plasma membrane;neuron projection;neuronal cell body;extracellular exosome
• Molecular function: protein tyrosine phosphatase activity;transmembrane receptor protein tyrosine phosphatase activity;heparin binding;chondroitin sulfate proteoglycan binding;protein-containing complex binding;cell adhesion molecule binding