PTPRQ

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

Basic information

Region (hg38): 12:80402178-80680273

Previous symbols: [ "DFNB84" ]

Links

ENSG00000139304 ∙ NCBI:374462 ∙ OMIM:603317 ∙ HGNC:9679 ∙ Uniprot:Q9UMZ3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive nonsyndromic hearing loss 84A (Strong), mode of inheritance: AR
• hearing loss, autosomal dominant 73 (Moderate), mode of inheritance: AD
• autosomal recessive nonsyndromic hearing loss 84A (Moderate), mode of inheritance: Semidominant
• autosomal dominant nonsyndromic hearing loss (Supportive), mode of inheritance: AD
• hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
• autosomal recessive nonsyndromic hearing loss 84A (Strong), mode of inheritance: AR
• hearing loss, autosomal dominant 73 (Limited), mode of inheritance: Unknown
• hearing loss, autosomal recessive (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal recessive 84	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic	19888295; 20346435
In Deafness, autosomal dominant 73, the onset of hearing loss has been described as variable but typically postlingual

ClinVar

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

• not provided (4 variants)
• Autosomal recessive nonsyndromic hearing loss 84A (2 variants)
• 7 conditions (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRQ 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	26	11	45
missense		1	90	16	29	136
nonsense	2	2	1		1	6
start loss		1				1
frameshift	3	6	1			10
inframe indel			1	1		2
splice donor/acceptor (+/-2bp)	1	2	1	1		5
splice region		1	5	8	1	15
non coding			4	51	105	160
Total	6	12	106	95	146

Highest pathogenic variant AF is 0.0000263

Variants in PTPRQ

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

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

Position	Type	Phenotype	Significance	ClinVar
12-80425096-A-G		not specified	Benign (-)
12-80436384-T-C			Likely benign (May 01, 2023)
12-80444099-G-C			Benign (Dec 22, 2018)
12-80444130-T-TA			Benign (Aug 18, 2019)
12-80444133-T-TA			Likely benign (Mar 13, 2020)
12-80444134-T-A			Benign (Aug 18, 2019)
12-80444137-T-A			Likely benign (Mar 13, 2020)
12-80444138-T-A			Benign (Aug 18, 2019)
12-80444141-T-A			Likely benign (Mar 13, 2020)
12-80444232-T-C			Benign (Nov 12, 2018)
12-80444345-G-A			Uncertain significance (Feb 01, 2022)
12-80444348-G-A		Hearing loss, autosomal dominant 73	Likely pathogenic (Jan 01, 2019)
12-80444384-G-C			Likely benign (Dec 15, 2020)
12-80444395-C-T		not specified	Benign (Dec 06, 2018)
12-80444396-A-C			Likely benign (Nov 01, 2023)
12-80444406-C-T		PTPRQ-related disorder	Likely benign (Jun 11, 2019)
12-80444407-G-A		PTPRQ-related disorder	Conflicting classifications of pathogenicity (Sep 01, 2019)
12-80444574-T-TATATG			Benign (Dec 17, 2018)
12-80444759-G-A		Inborn genetic diseases	Uncertain significance (Mar 01, 2023)
12-80444765-G-C		Inborn genetic diseases	Uncertain significance (Aug 10, 2021)
12-80444776-C-T		PTPRQ-related disorder	Likely benign (Jan 03, 2020)
12-80444784-C-T		not specified	Benign (Dec 06, 2018)
12-80444787-T-G			Uncertain significance (Jul 12, 2022)
12-80444811-C-T		Inborn genetic diseases	Uncertain significance (Dec 20, 2022)
12-80444829-T-C		Inborn genetic diseases	Likely benign (Sep 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPRQ	protein_coding	protein_coding	ENST00000266688	50	273029

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.22e-21	1.00	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.999	838	923	0.908	0.0000450	14874
Missense in Polyphen		285	337.62	0.84414		5371
Synonymous	0.177	324	328	0.988	0.0000174	4365
Loss of Function	3.93	48	87.8	0.547	0.00000440	1494

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phosphatidylinositol phosphatase required for auditory function. May act by regulating the level of phosphatidylinositol 4,5-bisphosphate (PIP2) level in the basal region of hair bundles. Can dephosphorylate a broad range of phosphatidylinositol phosphates, including phosphatidylinositol 3,4,5-trisphosphate and most phosphatidylinositol monophosphates and diphosphates. Phosphate can be hydrolyzed from the D3 and D5 positions in the inositol ring. Has low tyrosine-protein phosphatase activity; however, the relevance of such activity in vivo is unclear. Plays an important role in adipogenesis of mesenchymal stem cells (MSCs). Regulates the phosphorylation state of AKT1 by suppressing the phosphatidylinositol 3,4,5-trisphosphate (PIP3) level in MSCs and preadipocyte cells. {ECO:0000269|PubMed:19351528}.
• Disease: DISEASE: Deafness, autosomal recessive, 84A (DFNB84A) [MIM:613391]: A form of non-syndromic deafness characterized by progressive, sensorineural hearing loss and vestibular dysfunction. {ECO:0000269|PubMed:20346435, ECO:0000269|PubMed:20472657}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Deafness, autosomal dominant, 73 (DFNA73) [MIM:617663]: A form of non-syndromic hearing loss characterized by mild to severe bilateral symptoms with variable age of onset from early childhood to the third decade. {ECO:0000269|PubMed:29309402}. Note=The disease may be caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.105

Haploinsufficiency Scores

• pHI: 0.396

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.135

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptprq
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); hearing/vestibular/ear phenotype

Gene ontology

• Biological process: peptidyl-tyrosine dephosphorylation;regulation of fat cell differentiation
• Cellular component: integral component of membrane
• Molecular function: protein tyrosine phosphatase activity