SIGLEC5
protein-codingsialic acid binding Ig like lectin 5, the group of V-set domain containing|CD molecules|Sialic acid binding Ig like lectins
Gene summary
This gene encodes a member of the sialic acid-binding immunoglobulin-like lectin (Siglec) 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. The encoded protein is a member of the CD33-related subset of Siglecs and inhibits the activation of several cell types including monocytes, macrophages and neutrophils. Binding of group B Streptococcus (GBS) to the encoded protein plays a role in GBS immune evasion. [provided by RefSeq, Feb 2012]
- CD33L2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~15.4 kbGenCC 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 SIGLEC5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003830.4. 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 | 1 | 2 | |||
| missense | 78 | 6 | 1 | 85 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 80 | 6 | 2 | 88 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003821.1 | 9 | MANE Select | |
| Ensembl | ENSP00000507738.1 | 9 | MANE Select | |
| RefSeq | NP_001371637.1 | 8 | Standard | |
| RefSeq | NP_001371638.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Neutrophil degranulation
- Innate Immune System
- Immune System
- Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
- Adaptive Immune System
Biological Process
- cell adhesion
- neutrophil degranulation
Molecular Function
- protein binding
- carbohydrate binding
Cellular Component
- plasma membrane
- integral component of membrane
- secretory granule membrane
- tertiary granule membrane
- ficolin-1-rich granule membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000570106
- Coding exons
- 9
- Length
- 35371
- Individuals with no LoFs
- 122279
- Homozygous LoFs
- 195
- Heterozygous LoFs
- 3273
- Defined
- 125747
- p
- 0.0139
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.243 | 299 | 287 | 1.04 | 0.0000163 | 3498 |
| Missense (PolyPhen) | 64 | 73.926 | 0.86573 | 1022 | ||
| Synonymous | 0.635 | 113 | 122 | 0.927 | 0.00000725 | 1141 |
| Loss of Function | 1.63 | 12 | 19.8 | 0.606 | 9.83e-7 | 254 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.15 | 0.13 | notable |
| Latino/Admixed American | 0.011 | 0.011 | notable |
| Ashkenazi Jewish | 0.024 | 0.023 | notable |
| East Asian | 0.00017 | 0.00016 | rare |
| Finnish | 0.0056 | 0.0056 | notable |
| European (Non-Finnish) | 0.0052 | 0.0051 | notable |
| South Asian | 0.0043 | 0.0042 | notable |
| Other | 0.010 | 0.0098 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Putative adhesion molecule that mediates sialic-acid dependent binding to cells. Binds equally to alpha-2,3-linked and 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
- 0.0687
Intolerance Scores
- LoFtool
- 0.676
- RVIS EVS
- 0.55
- RVIS percentile EVS
- 81.6
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |