ITLN2

protein-coding

intelectin 2, the group of Fibrinogen C domain containing

Gene summary

Predicted to enable oligosaccharide binding activity. Predicted to be located in extracellular region. Predicted to be active in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_080878.3

Inheritance

—

ClinVar variants

U:57B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.68

Max pathogenic AF

—

Genomic locus

chr1:160,945,025-160,954,809

External References & Databases

Ensembl (ENSG00000158764)

Transcript & Mutation Effects

hg38 • Region Span ~9.8 kb

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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 ITLN2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 60

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_080878.3. 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			56 clinvar	5 clinvar	1 clinvar	62
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	57	5	3	65

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_080878.3	RefSeq	NP_543154.1	8	MANE Select
ENST00000368029.4	Ensembl	ENSP00000357008.3	8	MANE Select
ENST00000934771.1	Ensembl	ENSP00000604830.1	8	Standard
ENST00000934772.1	Ensembl	ENSP00000604831.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

EGFR1

Molecular Function

carbohydrate binding
metal ion binding

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368029
Coding exons: 8
Length: 9775
Individuals with no LoFs: 125703
Homozygous LoFs: 0
Heterozygous LoFs: 45
Defined: 125748
p: 0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.330	180	193	0.933	0.0000109	2124
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00016	0.00016	rare
Finnish	0.000052	0.000046	rare
European (Non-Finnish)	0.00023	0.00023	rare
South Asian	0.00023	0.00023	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in the defense system against pathogens. {ECO:0000250}.;

Recessive Scores

pRec: 0.0758

Intolerance Scores

LoFtool: 0.611
RVIS EVS: 0.8
RVIS percentile EVS: 87.59

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.137

Gene Damage Prediction

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