TINAGL1

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

Basic information

Region (hg38): 1:31576485-31587686

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.

not_specified (58 variants)
not_provided (2 variants)

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. These statistics are base on transcript: NM_000022164.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			52 clinvar	6 clinvar		58
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	52	8	0

Loading clinvar variants...

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