ITLN1
Basic information
Region (hg38): 1:160876540-160885180
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (46 variants)
- not_provided (6 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITLN1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017625.3. 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 | 5 | |||||
| missense | 44 | 47 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 44 | 3 | 5 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ITLN1 | protein_coding | protein_coding | ENST00000326245 | 7 | 8632 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000341 | 0.811 | 125700 | 0 | 47 | 125747 | 0.000187 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.430 | 174 | 191 | 0.912 | 0.0000110 | 2057 |
| Missense in Polyphen | 57 | 74.743 | 0.76262 | 873 | ||
| Synonymous | -1.02 | 85 | 73.8 | 1.15 | 0.00000481 | 583 |
| Loss of Function | 1.34 | 11 | 17.0 | 0.649 | 9.19e-7 | 178 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00144 | 0.00144 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000326 | 0.000326 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000115 | 0.000114 |
| Middle Eastern | 0.000326 | 0.000326 |
| South Asian | 0.000131 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Lectin that specifically recognizes microbial carbohydrate chains in a calcium-dependent manner (PubMed:11313366, PubMed:26148048). Binds to microbial glycans that contain a terminal acyclic 1,2-diol moiety, including beta- linked D-galactofuranose (beta-Galf), D-phosphoglycerol-modified glycans, D-glycero-D-talo-oct-2-ulosonic acid (KO) and 3-deoxy-D- manno-oct-2-ulosonic acid (KDO) (PubMed:26148048). Binds to glycans from Gram-positive and Gram-negative bacteria, including K.pneumoniae, S.pneumoniae, Y.pestis, P.mirabilis and P.vulgaris (PubMed:26148048). Does not bind human glycans (PubMed:26148048). Probably plays a role in the defense system against microorganisms (Probable). May function as adipokine that has no effect on basal glucose uptake but enhances insulin-stimulated glucose uptake in adipocytes (PubMed:16531507). Increases AKT phosphorylation in the absence and presence of insulin (PubMed:16531507). May interact with lactoferrin/LTF and increase its uptake, and may thereby play a role in iron absorption (PubMed:11747454, PubMed:23921499). {ECO:0000269|PubMed:11313366, ECO:0000269|PubMed:16531507, ECO:0000269|PubMed:23921499, ECO:0000269|PubMed:26148048, ECO:0000305, ECO:0000305|PubMed:11747454}.;
- Pathway
- Antimicrobial peptides;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.153
Intolerance Scores
- loftool
- 0.422
- rvis_EVS
- -0.44
- rvis_percentile_EVS
- 24.46
Haploinsufficiency Scores
- pHI
- 0.0768
- hipred
- N
- hipred_score
- 0.132
- ghis
- 0.407
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0401
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Itln1
- Phenotype
- normal phenotype;
Gene ontology
- Biological process
- positive regulation of protein phosphorylation;response to nematode;antimicrobial humoral response;positive regulation of glucose import;protein homotrimerization
- Cellular component
- extracellular region;anchored component of membrane;brush border membrane;receptor complex;membrane raft;extracellular exosome
- Molecular function
- calcium ion binding;identical protein binding;oligosaccharide binding