TPRN

taperin

Basic information

Region (hg38): 9:137191616-137204193

Previous symbols: [ "C9orf75", "DFNB79" ]

Links

ENSG00000176058 ∙ NCBI:286262 ∙ OMIM:613354 ∙ HGNC:26894 ∙ Uniprot:Q4KMQ1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive nonsyndromic hearing loss 79 (Strong), mode of inheritance: AR
• autosomal recessive nonsyndromic hearing loss 79 (Strong), mode of inheritance: AR
• hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
• nonsyndromic genetic hearing loss (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal recessive 79	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic	19603065; 20170898; 23340767

ClinVar

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

• not provided (196 variants)
• Inborn genetic diseases (50 variants)
• not specified (29 variants)
• Autosomal recessive nonsyndromic hearing loss 79 (14 variants)
• TPRN-related condition (1 variants)
• Ear malformation (1 variants)
• Hearing impairment (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPRN 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			3	43	5	51
missense			105	10	5	120
nonsense	3					3
start loss						0
frameshift	5	3				8
inframe indel			12	3	4	19
splice donor/acceptor (+/-2bp)						0
splice region			2	1		3
non coding			1	9	4	14
Total	8	3	121	65	18

Highest pathogenic variant AF is 0.000192

Variants in TPRN

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

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

Position	Type	Phenotype	Significance	ClinVar
9-137192121-C-G			Likely benign (May 01, 2022)
9-137192122-A-G		Inborn genetic diseases	Uncertain significance (Aug 20, 2023)
9-137192133-G-A			Likely benign (Jul 10, 2023)
9-137192137-C-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Dec 06, 2023)
9-137192138-G-A			Uncertain significance (Jan 05, 2022)
9-137192142-G-A			Likely benign (May 19, 2021)
9-137192165-C-T		not specified	Uncertain significance (Feb 04, 2015)
9-137192179-A-G		not specified	Uncertain significance (Mar 01, 2019)
9-137192184-A-T			Likely benign (Jul 19, 2022)
9-137192192-G-T			Likely benign (Jun 18, 2021)
9-137192205-T-C			Likely benign (Aug 28, 2020)
9-137192237-G-A			Likely benign (Dec 12, 2020)
9-137192249-C-G			Benign (Dec 16, 2023)
9-137192249-C-T		not specified	Likely benign (Aug 04, 2016)
9-137192250-G-A			Uncertain significance (Sep 25, 2015)
9-137192270-C-T		Inborn genetic diseases	Uncertain significance (Feb 14, 2023)
9-137192271-G-A			Likely benign (Apr 09, 2023)
9-137192275-G-A		not specified • Autosomal recessive nonsyndromic hearing loss 79	Likely benign (Oct 06, 2016)
9-137192278-G-A			Uncertain significance (Aug 19, 2022)
9-137192292-C-T			Likely benign (Apr 29, 2022)
9-137192293-G-A		Inborn genetic diseases	Uncertain significance (Dec 20, 2021)
9-137192299-T-C			Uncertain significance (Sep 26, 2022)
9-137192305-AGCGCCTGCTCCT-A			Uncertain significance (Sep 14, 2021)
9-137192307-C-T			Likely benign (Jun 16, 2022)
9-137192308-G-A			Uncertain significance (Jun 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPRN	protein_coding	protein_coding	ENST00000409012	4	12577

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00722	0.978	125525	0	38	125563	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.497	307	283	1.08	0.0000168	4430
Missense in Polyphen		106	101.92	1.04		1292
Synonymous	-1.91	160	132	1.21	0.00000885	1613
Loss of Function	2.13	6	14.9	0.403	6.86e-7	209

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000281	0.000273
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000584	0.0000544
Finnish	0.0000469	0.0000462
European (Non-Finnish)	0.000202	0.000194
Middle Eastern	0.0000584	0.0000544
South Asian	0.000262	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.118
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

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

Gene ontology

• Biological process: sensory perception of sound;stereocilium maintenance
• Cellular component: stereocilium
• Molecular function: molecular_function;protein binding;phosphatase binding