SIGLEC11

protein-coding

sialic acid binding Ig like lectin 11, the group of V-set domain containing|C2-set domain containing|Sialic acid binding Ig like lectins|I-set domain containing

Gene summary

This gene encodes a member of the sialic acid-binding immunoglobulin-like lectin family. These cell surface lectins are characterized by structural motifs in the immunoglobulin (Ig)-like domains and sialic acid recognition sites in the first Ig V set domain. This family member mediates anti-inflammatory and immunosuppressive signaling. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

MANE transcript

NM_052884.3

Inheritance

—

ClinVar variants

U:135B:22

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.15

Max pathogenic AF

—

Genomic locus

chr19:49,948,985-49,961,172

External References & Databases

Ensembl (ENSG00000161640)

Transcript & Mutation Effects

hg38 • Region Span ~12.2 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 SIGLEC11 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 148

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052884.3. 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	5 clinvar	1 clinvar	7
missense			133 clinvar	15 clinvar	1 clinvar	149
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	135	20	2	157

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052884.3	RefSeq	NP_443116.2	11	MANE Select
ENST00000447370.6	Ensembl	ENSP00000412361.2	11	MANE Select
NM_001135163.1	RefSeq	NP_001128635.1	10	Standard
ENST00000426296.1	Ensembl	ENSP00000407387.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Immune System
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
Adaptive Immune System

Biological Process

multi organism cell adhesion
negative regulation of defense response to bacterium

Molecular Function

phosphatase binding
carbohydrate binding
sialic acid binding

Cellular Component

cell surface
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000447370
Coding exons: 11
Length: 12188
Individuals with no LoFs: 125547
Homozygous LoFs: 1
Heterozygous LoFs: 200
Defined: 125748
p: 0.000800

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.950	421	370	1.14	0.0000218	4415
Missense (PolyPhen)		101	99.245	1.0177		1336
Synonymous	-1.97	199	167	1.19	0.0000108	1459
Loss of Function	-0.718	30	26.0	1.15	0.00000141	298

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0014	0.0012	notable
Latino/Admixed American	0.00047	0.00046	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0026	0.0026	notable
Finnish	0.00024	0.00023	rare
European (Non-Finnish)	0.00068	0.00065	rare
South Asian	0.0014	0.0012	notable
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Putative adhesion molecule that mediates sialic-acid dependent binding to cells. Preferentially binds to alpha-2,8- linked sialic acid. The sialic acid recognition site may be masked by cis interactions with sialic acids on the same cell surface. In the immune response, may act as an inhibitory receptor upon ligand induced tyrosine phosphorylation by recruiting cytoplasmic phosphatase(s) via their SH2 domain(s) that block signal transduction through dephosphorylation of signaling molecules.;

Recessive Scores

pRec: 0.0827

Intolerance Scores

LoFtool: 0.960
RVIS EVS: 0.85
RVIS percentile EVS: 88.48

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.515

Gene Damage Prediction

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