TINAG
protein-codingtubulointerstitial nephritis antigen, the group of Peptidase family C1
Gene summary
This gene encodes a glycoprotein that is restricted within the kidney to the basement membranes underlying the epithelium of Bowman's capsule and proximal and distal tubules. Autoantibodies against this protein are found in sera of patients with tubulointerstital nephritis, membranous nephropathy and anti-glomerular basement membrane nephritis. Ontogeny studies suggest that the expression of this antigen is developmentally regulated in a precise spatial and temporal pattern throughout nephrogenesis. [provided by RefSeq, Nov 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~82.3 kbGenCC 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 TINAG variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014464.4. 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 | 1 | ||||
| missense | 71 | 5 | 76 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 73 | 5 | 1 | 79 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055279.3 | 11 | MANE Select | |
| Ensembl | ENSP00000259782.4 | 11 | MANE Select | |
| Ensembl | ENSP00000359901.3 | 4 | Standard | |
| Ensembl | ENSP00000359906.3 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- proteolysis
- receptor-mediated endocytosis
- immune response
- cell adhesion
Molecular Function
- nucleotide binding
- cysteine-type endopeptidase activity
- scavenger receptor activity
- polysaccharide binding
Cellular Component
- basement membrane
- extracellular space
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000259782
- Coding exons
- 11
- Length
- 82294
- Individuals with no LoFs
- 125532
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 210
- Defined
- 125744
- p
- 0.000843
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.17 | 314 | 261 | 1.20 | 0.0000138 | 3118 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00054 | 0.00052 | rare |
| Ashkenazi Jewish | 0.00082 | 0.00079 | rare |
| East Asian | 0.0017 | 0.0016 | notable |
| Finnish | 0.000099 | 0.000092 | rare |
| European (Non-Finnish) | 0.00079 | 0.00077 | rare |
| South Asian | 0.0020 | 0.0019 | notable |
| Other | 0.00082 | 0.00081 | rare |
dbNSFP Gene Annotations
Source:
- 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
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.138
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |