ITLN1

intelectin 1

Basic information

Region (hg38): 1:160876540-160885180

Links

ENSG00000179914 ∙ NCBI:55600 ∙ OMIM:609873 ∙ HGNC:18259 ∙ Uniprot:Q8WWA0 ∙ 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 ITLN1 gene.

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.

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					5	5
missense			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	5

Variants in ITLN1

This is a list of pathogenic ClinVar variants found in the ITLN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-160876668-C-G			Likely benign (May 31, 2018)
1-160876714-T-C		not specified	Uncertain significance (Jun 17, 2022)
1-160876732-C-G		not specified	Uncertain significance (Apr 12, 2022)
1-160879328-C-T		not specified	Uncertain significance (Apr 18, 2023)
1-160879371-G-A			Benign (Jul 31, 2018)
1-160880643-G-T			Benign (Jul 04, 2018)
1-160880679-C-A		not specified	Uncertain significance (Oct 04, 2022)
1-160881156-G-C		not specified	Uncertain significance (Jun 13, 2022)
1-160881206-G-A		not specified	Uncertain significance (Jul 13, 2021)
1-160881265-G-A			Benign (Oct 19, 2017)
1-160881963-G-C		not specified	Uncertain significance (Jun 09, 2022)
1-160882020-G-A			Benign (Jul 31, 2018)
1-160882090-C-T		not specified	Likely benign (Jan 31, 2022)
1-160882103-C-T		not specified	Uncertain significance (Aug 08, 2022)
1-160882130-C-T		not specified	Uncertain significance (Jul 12, 2022)
1-160882135-C-A		not specified	Uncertain significance (Nov 08, 2022)
1-160882144-G-C		not specified	Uncertain significance (Nov 21, 2022)
1-160882177-T-C		not specified	Uncertain significance (May 24, 2024)
1-160882184-T-G		not specified	Uncertain significance (Dec 02, 2022)
1-160883521-C-A		not specified	Uncertain significance (Feb 12, 2024)
1-160883522-C-T			Benign (Apr 24, 2018)
1-160884849-A-G		not specified	Uncertain significance (Nov 07, 2022)
1-160884870-T-G		not specified	Uncertain significance (Jun 21, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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