ITLN2

intelectin 2, the group of Fibrinogen C domain containing

Basic information

Region (hg38): 1:160945024-160954809

Links

ENSG00000158764 ∙ NCBI:142683 ∙ OMIM:609874 ∙ HGNC:20599 ∙ Uniprot:Q8WWU7 ∙ 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 ITLN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITLN2 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					2	2
missense			25	4	1	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	4	3

Variants in ITLN2

This is a list of pathogenic ClinVar variants found in the ITLN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-160945156-A-G		not specified	Uncertain significance (Sep 16, 2021)
1-160945181-G-A		not specified	Uncertain significance (Jun 28, 2022)
1-160945215-A-T		not specified	Uncertain significance (Mar 31, 2024)
1-160945226-A-G		not specified	Uncertain significance (Jun 24, 2022)
1-160945249-C-T		not specified	Uncertain significance (Apr 19, 2023)
1-160945250-G-A		not specified	Likely benign (Nov 08, 2022)
1-160945252-G-A		not specified	Uncertain significance (Oct 13, 2023)
1-160947942-C-G		not specified	Uncertain significance (Oct 25, 2023)
1-160947984-C-G		not specified	Uncertain significance (Mar 29, 2022)
1-160947989-G-C		not specified	Likely benign (May 20, 2024)
1-160950057-G-A		not specified	Uncertain significance (Dec 12, 2023)
1-160950134-A-C		not specified	Uncertain significance (Apr 30, 2024)
1-160950582-G-A			Benign (Dec 14, 2017)
1-160950599-G-C		not specified	Uncertain significance (Apr 28, 2022)
1-160950637-A-T		not specified	Uncertain significance (Sep 12, 2023)
1-160950641-T-C			Benign (Dec 14, 2017)
1-160950648-G-A		not specified	Uncertain significance (Mar 01, 2023)
1-160950674-C-T		not specified	Uncertain significance (Mar 13, 2023)
1-160950689-T-C		not specified	Uncertain significance (Apr 20, 2024)
1-160950693-T-C		not specified	Uncertain significance (Feb 21, 2024)
1-160951048-A-G		not specified	Uncertain significance (Apr 22, 2022)
1-160951056-C-T		not specified	Uncertain significance (May 04, 2022)
1-160951065-G-A		not specified	Uncertain significance (Sep 06, 2022)
1-160951075-A-G		not specified	Uncertain significance (Aug 30, 2021)
1-160951112-C-T			Benign (Dec 14, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITLN2	protein_coding	protein_coding	ENST00000368029	8	9775

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000245	0.749	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.330	180	193	0.933	0.0000109	2124
Missense in Polyphen		55	59.877	0.91855		725
Synonymous	-0.430	81	76.2	1.06	0.00000488	607
Loss of Function	1.21	11	16.3	0.676	7.88e-7	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000301	0.000300
Ashkenazi Jewish	0.0000998	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000521	0.0000462
European (Non-Finnish)	0.000231	0.000229
Middle Eastern	0.000163	0.000163
South Asian	0.000229	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the defense system against pathogens. {ECO:0000250}.
• Pathway: EGFR1 (Consensus)

Recessive Scores

• pRec: 0.0758

Intolerance Scores

• loftool: 0.611
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.59

Haploinsufficiency Scores

• pHI: 0.0240
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.137

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

• Cellular component: extracellular region
• Molecular function: carbohydrate binding;metal ion binding