TINAG

tubulointerstitial nephritis antigen, the group of Peptidase family C1

Basic information

Region (hg38): 6:54307858-54390142

Links

ENSG00000137251 ∙ NCBI:27283 ∙ OMIM:606749 ∙ HGNC:14599 ∙ Uniprot:Q9UJW2 ∙ 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 TINAG gene.

• Inborn genetic diseases (23 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TINAG 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					1	1
missense			19	4		23
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	4	1

Variants in TINAG

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

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

Position	Type	Phenotype	Significance	ClinVar
6-54308583-T-G			Benign (Mar 29, 2018)
6-54308687-G-C		not specified	Uncertain significance (Dec 21, 2023)
6-54308698-G-C		not specified	Uncertain significance (Oct 06, 2021)
6-54308833-T-C		not specified	Uncertain significance (Oct 22, 2021)
6-54308875-C-G		not specified	Uncertain significance (Dec 20, 2023)
6-54308876-C-T		not specified	Uncertain significance (Oct 14, 2021)
6-54321304-T-A		not specified	Uncertain significance (Feb 28, 2023)
6-54321358-A-G		not specified	Uncertain significance (Jul 29, 2022)
6-54321376-G-A		not specified	Uncertain significance (Dec 08, 2021)
6-54326914-A-T		not specified	Uncertain significance (Feb 17, 2024)
6-54343226-G-A		not specified	Uncertain significance (Jan 05, 2022)
6-54343265-G-A		not specified	Likely benign (Dec 02, 2022)
6-54343283-C-T		not specified	Uncertain significance (Feb 28, 2024)
6-54343313-A-G		not specified	Uncertain significance (Jun 21, 2023)
6-54343316-A-C		not specified	Uncertain significance (Jan 19, 2024)
6-54343319-T-C		not specified	Uncertain significance (Nov 13, 2023)
6-54347486-G-A		not specified	Uncertain significance (Mar 13, 2023)
6-54347489-A-G		not specified	Uncertain significance (Jan 23, 2024)
6-54349729-G-A		not specified	Uncertain significance (Feb 06, 2023)
6-54349769-A-G		not specified	Likely benign (Feb 16, 2023)
6-54349781-T-C		not specified	Uncertain significance (Dec 30, 2023)
6-54349791-G-T		not specified	Uncertain significance (Jul 27, 2021)
6-54349804-G-A		not specified	Uncertain significance (Feb 05, 2024)
6-54349828-T-C		not specified	Uncertain significance (Oct 29, 2021)
6-54349840-G-A		not specified	Likely benign (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TINAG	protein_coding	protein_coding	ENST00000259782	11	82294

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.43e-25	0.000135	125532	2	210	125744	0.000843

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.17	314	261	1.20	0.0000138	3118
Missense in Polyphen		105	97.028	1.0822		1111
Synonymous	-0.902	100	89.2	1.12	0.00000493	830
Loss of Function	-0.401	36	33.5	1.07	0.00000195	360

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000784	0.000782
Ashkenazi Jewish	0.000822	0.000794
East Asian	0.00175	0.00158
Finnish	0.0000990	0.0000924
European (Non-Finnish)	0.000791	0.000765
Middle Eastern	0.00175	0.00158
South Asian	0.00201	0.00193
Other	0.000825	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates adhesion of proximal tubule epithelial cells via integrins alpha3-beta1 and alphaV-beta3. This is a non catalytic peptidase C1 family protein. {ECO:0000269|PubMed:8770961}.

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.331
• rvis_EVS: 1.07
• rvis_percentile_EVS: 91.67

Haploinsufficiency Scores

• pHI: 0.193
• hipred: N
• hipred_score: 0.219

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.138

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tinag

Gene ontology

• Biological process: proteolysis;receptor-mediated endocytosis;immune response;cell adhesion
• Cellular component: basement membrane;extracellular space
• Molecular function: nucleotide binding;cysteine-type endopeptidase activity;scavenger receptor activity;polysaccharide binding