SIGLEC1

sialic acid binding Ig like lectin 1, the group of V-set domain containing|CD molecules|C2-set domain containing|Sialic acid binding Ig like lectins|I-set domain containing

Basic information

Region (hg38): 20:3686969-3712600

Previous symbols: [ "SN" ]

Links

ENSG00000088827 ∙ NCBI:6614 ∙ OMIM:600751 ∙ HGNC:11127 ∙ Uniprot:Q9BZZ2 ∙ 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 SIGLEC1 gene.

• Inborn genetic diseases (87 variants)
• not provided (26 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIGLEC1 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				9	5	14
missense			81	12	1	94
nonsense					1	1
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	81	21	8

Variants in SIGLEC1

This is a list of pathogenic ClinVar variants found in the SIGLEC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-3688588-GT-G			Benign (Dec 31, 2019)
20-3688615-A-G		not specified	Uncertain significance (Dec 22, 2023)
20-3689187-C-T		not specified	Uncertain significance (Jun 13, 2023)
20-3689196-C-G		not specified	Conflicting classifications of pathogenicity (Jun 07, 2022)
20-3689999-C-T			Benign (Dec 31, 2019)
20-3690126-T-A		not specified	Uncertain significance (Jun 22, 2023)
20-3690171-G-A		not specified	Uncertain significance (Jun 18, 2021)
20-3690192-C-T		not specified	Uncertain significance (Feb 24, 2023)
20-3690213-A-T		not specified	Uncertain significance (Nov 27, 2023)
20-3691352-G-A		not specified	Uncertain significance (Sep 16, 2021)
20-3691399-C-T			Likely benign (Feb 01, 2023)
20-3691409-T-G		not specified	Likely benign (Nov 09, 2023)
20-3691423-C-T		not specified	Uncertain significance (Apr 05, 2023)
20-3691430-C-T		not specified	Uncertain significance (Nov 17, 2022)
20-3691442-C-T		not specified	Likely benign (May 08, 2023)
20-3691463-C-T			Likely benign (Mar 01, 2023)
20-3691471-C-T		not specified	Likely benign (Oct 24, 2023)
20-3691476-G-A			Likely benign (Mar 01, 2023)
20-3691487-A-G		not specified	Uncertain significance (Sep 12, 2023)
20-3691497-G-T			Likely benign (Feb 01, 2023)
20-3691522-C-T		not specified	Uncertain significance (Jul 19, 2022)
20-3691580-G-A		not specified	Uncertain significance (Oct 26, 2022)
20-3691922-G-A			Likely benign (Mar 01, 2023)
20-3691923-A-G		not specified	Likely benign (Dec 07, 2021)
20-3692004-C-T		not specified	Uncertain significance (Mar 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIGLEC1	protein_coding	protein_coding	ENST00000344754	21	20159

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.33e-46	1.84e-7	122940	26	2782	125748	0.0112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.277	1075	1.05e+3	1.02	0.0000673	10778
Missense in Polyphen		297	322.19	0.92183		3696
Synonymous	0.114	446	449	0.993	0.0000286	3823
Loss of Function	-0.0527	69	68.5	1.01	0.00000391	681

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0119	0.0119
Ashkenazi Jewish	0.00938	0.00917
East Asian	0.00652	0.00644
Finnish	0.00242	0.00241
European (Non-Finnish)	0.0150	0.0148
Middle Eastern	0.00652	0.00644
South Asian	0.0146	0.0143
Other	0.0144	0.0143

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as an endocytic receptor mediating clathrin dependent endocytosis. Macrophage-restricted adhesion molecule that mediates sialic-acid dependent binding to lymphocytes, including granulocytes, monocytes, natural killer cells, B-cells and CD8 T-cells. Preferentially binds to alpha-2,3-linked sialic acid (By similarity). Binds to SPN/CD43 on T-cells (By similarity). May play a role in hemopoiesis. {ECO:0000250}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.208

Intolerance Scores

• loftool: 0.916
• rvis_EVS: -1.81
• rvis_percentile_EVS: 2.19

Haploinsufficiency Scores

• pHI: 0.113
• hipred: N
• hipred_score: 0.123
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.154

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Siglec1
• Phenotype: immune system phenotype; homeostasis/metabolism phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: endocytosis;inflammatory response;cell-matrix adhesion;cell-cell adhesion
• Cellular component: extracellular region;plasma membrane;integral component of membrane
• Molecular function: carbohydrate binding