TINAGL1

tubulointerstitial nephritis antigen like 1, the group of Peptidase family C1

Basic information

Region (hg38): 1:31576484-31587686

Previous symbols: [ "LCN7" ]

Links

ENSG00000142910 ∙ NCBI:64129 ∙ OMIM:616064 ∙ HGNC:19168 ∙ Uniprot:Q9GZM7 ∙ 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 TINAGL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TINAGL1 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				2		2
missense			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	4	0

Variants in TINAGL1

This is a list of pathogenic ClinVar variants found in the TINAGL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-31577204-C-T		not specified	Uncertain significance (Jun 27, 2022)
1-31577215-C-G		not specified	Uncertain significance (Feb 12, 2024)
1-31577231-G-A		not specified	Uncertain significance (Jun 05, 2023)
1-31577232-C-T			Likely benign (Jul 10, 2018)
1-31577270-G-A		not specified	Uncertain significance (Sep 30, 2021)
1-31577276-C-T		not specified	Uncertain significance (Sep 01, 2021)
1-31577281-G-A		not specified	Uncertain significance (Sep 22, 2022)
1-31577284-C-T		not specified	Uncertain significance (Apr 18, 2023)
1-31577285-G-A		not specified	Uncertain significance (Jan 09, 2024)
1-31577329-G-T		not specified	Uncertain significance (Oct 06, 2021)
1-31577339-T-G		not specified	Uncertain significance (Jun 28, 2022)
1-31577437-C-T		not specified	Uncertain significance (Aug 12, 2021)
1-31579222-G-A		not specified	Uncertain significance (Dec 17, 2023)
1-31579228-A-C		not specified	Uncertain significance (Aug 02, 2022)
1-31579228-A-T		not specified	Uncertain significance (Apr 18, 2024)
1-31579249-G-T		not specified	Uncertain significance (May 26, 2024)
1-31583162-A-G		not specified	Uncertain significance (Mar 14, 2023)
1-31583228-C-G		not specified	Uncertain significance (Oct 03, 2022)
1-31583493-G-T		not specified	Uncertain significance (Mar 18, 2024)
1-31584682-T-C		not specified	Uncertain significance (Mar 20, 2024)
1-31584688-A-G		not specified	Uncertain significance (Jan 31, 2022)
1-31584896-C-T			Likely benign (Nov 01, 2022)
1-31585026-C-T		not specified	Uncertain significance (Jan 10, 2022)
1-31585180-C-T		not specified	Uncertain significance (Jan 10, 2023)
1-31585197-G-A		not specified	Likely benign (Nov 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TINAGL1	protein_coding	protein_coding	ENST00000271064	11	11173

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000329	0.999	125727	0	20	125747	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	246	309	0.796	0.0000207	3024
Missense in Polyphen		94	148.94	0.63114		1462
Synonymous	1.69	96	120	0.803	0.00000821	912
Loss of Function	3.05	11	28.6	0.384	0.00000166	273

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000303	0.000302
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000706	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.000100	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be implicated in the adrenocortical zonation and in mechanisms for repressing the CYP11B1 gene expression in adrenocortical cells. This is a non catalytic peptidase C1 family protein (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.375
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.12

Haploinsufficiency Scores

• pHI: 0.260
• hipred: Y
• hipred_score: 0.614
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.694

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tinagl1
• Phenotype: reproductive system phenotype; 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)

Zebrafish Information Network

• Gene name: tinagl1
• Affected structure: dorsal longitudinal anastomotic vessel
• Phenotype tag: abnormal
• Phenotype quality: immature

Gene ontology

• Biological process: proteolysis;receptor-mediated endocytosis;immune response;cell adhesion;endosomal transport
• Cellular component: extracellular region;extracellular space;cytoplasm;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: scavenger receptor activity;extracellular matrix structural constituent;protein binding;cysteine-type peptidase activity;polysaccharide binding;laminin binding