TINAGL1

protein-coding

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

Gene summary

The protein encoded by this gene is similar in sequence to tubulointerstitial nephritis antigen, a secreted glycoprotein that is recognized by antibodies in some types of immune-related tubulointerstitial nephritis. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2011]

Previous symbols:

LCN7

MANE transcript

NM_022164.3

Inheritance

—

ClinVar variants

U:68B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr1:31,576,485-31,587,686

External References & Databases

Ensembl (ENSG00000142910)

Transcript & Mutation Effects

hg38 • Region Span ~11.2 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TINAGL1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 69

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022164.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar		3
missense			64 clinvar	6 clinvar		70
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	68	8	0	76

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022164.3	RefSeq	NP_071447.1	11	MANE Select
ENST00000271064.12	Ensembl	ENSP00000271064.7	11	MANE Select
NM_001204414.2	RefSeq	NP_001191343.1	10	Standard
NM_001204415.2	RefSeq	NP_001191344.1	10	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
tinagl1	Danio rerio	Structure: dorsal longitudinal anastomotic vessel Quality: immature abnormal

Gene / Model

Organism

Observed Phenotype

tinagl1

Danio rerio

Structure: dorsal longitudinal anastomotic vessel

Quality: immature

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

proteolysis
receptor-mediated endocytosis
immune response
cell adhesion
endosomal transport

Molecular Function

scavenger receptor activity
extracellular matrix structural constituent
protein binding
cysteine-type peptidase activity
polysaccharide binding

Cellular Component

extracellular region
extracellular space
cytoplasm
collagen-containing extracellular matrix
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000271064
Coding exons: 11
Length: 11173
Individuals with no LoFs: 125727
Homozygous LoFs: 0
Heterozygous LoFs: 20
Defined: 125747
p: 0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.27	246	309	0.796	0.0000207	3024
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.00010	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.694

Gene Damage Prediction

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