SIGLEC6

protein-coding

sialic acid binding Ig like lectin 6, the group of V-set domain containing|CD molecules|Sialic acid binding Ig like lectins|I-set domain containing

Gene summary

This gene encodes a member of the SIGLEC (sialic acid binding immunoglobulin-like lectin) family of proteins. The encoded transmembrane receptor binds sialyl-TN glycans and leptin. Placental expression of the encoded protein is upregulated in preeclampsia. [provided by RefSeq, Jul 2016]

Previous symbols:

CD33L
CD33L1

MANE transcript

NM_001245.7

Inheritance

—

ClinVar variants

U:67B:7

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.37

Max pathogenic AF

—

Genomic locus

chr19:51,517,819-51,531,856

External References & Databases

Ensembl (ENSG00000105492)

Transcript & Mutation Effects

hg38 • Region Span ~14.0 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 SIGLEC6 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 70

not providedTotal: 3

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001245.7. 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						0
missense			67 clinvar	4 clinvar	3 clinvar	74
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	67	4	3	74

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001245.7	RefSeq	NP_001236.4	8	MANE Select
ENST00000425629.8	Ensembl	ENSP00000401502.2	8	MANE Select
NM_001177547.3	RefSeq	NP_001171018.1	7	Standard
NM_001177548.3	RefSeq	NP_001171019.1	7	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

cell adhesion
cell-cell signaling

Molecular Function

protein binding
carbohydrate binding

Cellular Component

extracellular region
integral component of plasma membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000425629
Coding exons: 8
Length: 12332
Individuals with no LoFs: 125703
Homozygous LoFs: 0
Heterozygous LoFs: 33
Defined: 125736
p: 0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.242	249	260	0.958	0.0000142	2897
Missense (PolyPhen)		44	58.315	0.75452		680
Synonymous	0.731	101	111	0.912	0.00000642	958
Loss of Function	2.51	7	18.7	0.374	8.85e-7	200

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00057	0.00055	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.000033	0.000033	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Putative adhesion molecule that mediates sialic-acid dependent binding to cells. Binds to alpha-2,6-linked sialic acid. The sialic acid recognition site may be masked by cis interactions with sialic acids on the same cell surface.;

Recessive Scores

pRec: 0.0710

Intolerance Scores

LoFtool: 0.883
RVIS EVS: 1.51
RVIS percentile EVS: 95.45

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.177

Gene Damage Prediction

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