SIGLEC5

sialic acid binding Ig like lectin 5, the group of V-set domain containing|CD molecules|Sialic acid binding Ig like lectins

Basic information

Region (hg38): 19:51630101-51645545

Previous symbols: [ "CD33L2" ]

Links

ENSG00000105501 ∙ NCBI:8778 ∙ OMIM:604200 ∙ HGNC:10874 ∙ Uniprot:O15389 ∙ 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 SIGLEC5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIGLEC5 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					1	1
missense			30	4	1	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	4	2

Variants in SIGLEC5

This is a list of pathogenic ClinVar variants found in the SIGLEC5 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-51630108-G-C		not specified	Uncertain significance (Feb 28, 2023)
19-51630168-A-G		not specified	Uncertain significance (Aug 09, 2021)
19-51630310-A-G		not specified	Uncertain significance (Jan 04, 2024)
19-51643372-C-T		not specified	Uncertain significance (Nov 10, 2022)
19-51643547-A-G		not specified	Uncertain significance (Jul 14, 2021)
19-51643805-T-A		not specified	Uncertain significance (Feb 27, 2023)
19-51643877-T-G		not specified	Uncertain significance (Aug 10, 2021)
19-51643933-C-A		not specified	Uncertain significance (Jan 16, 2024)
19-51644012-A-T		not specified	Uncertain significance (Jun 13, 2023)
19-51644020-G-A			Benign (Dec 20, 2017)
19-51644024-A-G		not specified	Uncertain significance (Mar 04, 2024)
19-51645527-G-T		not specified	Uncertain significance (May 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIGLEC5	protein_coding	protein_coding	ENST00000570106	9	35371

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000212	0.902	122279	195	3273	125747	0.0139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.243	299	287	1.04	0.0000163	3498
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.160	0.141
Ashkenazi Jewish	0.0236	0.0231
East Asian	0.000166	0.000163
Finnish	0.00560	0.00556
European (Non-Finnish)	0.00517	0.00508
Middle Eastern	0.000166	0.000163
South Asian	0.00430	0.00422
Other	0.0103	0.00982

dbNSFP

Source: dbNSFP

• 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.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.0687

Intolerance Scores

• loftool: 0.676
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.6

Haploinsufficiency Scores

• pHI: 0.0267
• hipred: N
• hipred_score: 0.164
• ghis: 0.460

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Siglecf
• Phenotype: cellular phenotype; respiratory system phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: cell adhesion;neutrophil degranulation
• Cellular component: plasma membrane;integral component of membrane;secretory granule membrane;tertiary granule membrane;ficolin-1-rich granule membrane
• Molecular function: protein binding;carbohydrate binding