SIGLEC6

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

Basic information

Region (hg38): 19:51517818-51531856

Previous symbols: [ "CD33L", "CD33L1" ]

Links

ENSG00000105492 ∙ NCBI:946 ∙ OMIM:604405 ∙ HGNC:10875 ∙ Uniprot:O43699 ∙ 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 SIGLEC6 gene.

• Inborn genetic diseases (15 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIGLEC6 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						0
missense			14	1	3	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	3

Variants in SIGLEC6

This is a list of pathogenic ClinVar variants found in the SIGLEC6 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-51520117-C-T		not specified	Likely benign (Nov 09, 2021)
19-51520123-C-A		not specified	Uncertain significance (Mar 24, 2023)
19-51520213-G-T		not specified	Uncertain significance (Apr 07, 2023)
19-51520234-T-C		not specified	Uncertain significance (Jul 09, 2021)
19-51527767-C-T		not specified	Uncertain significance (Aug 30, 2021)
19-51528185-A-C		not specified	Uncertain significance (Jan 16, 2024)
19-51528229-C-T			Benign (Sep 11, 2018)
19-51528236-C-T		not specified	Uncertain significance (Jan 17, 2024)
19-51529852-G-A		not specified	Uncertain significance (Feb 03, 2022)
19-51529853-C-A		Malignant tumor of prostate	Uncertain significance (-)
19-51530698-A-G		not specified	Uncertain significance (May 04, 2022)
19-51530720-C-T		not specified	Uncertain significance (Dec 08, 2022)
19-51530858-G-A		not specified	Uncertain significance (Aug 23, 2021)
19-51530860-G-A		not specified	Uncertain significance (Oct 12, 2021)
19-51530866-T-C		not specified	Uncertain significance (Jan 24, 2023)
19-51530935-G-C		not specified	Uncertain significance (Jan 26, 2023)
19-51531183-G-A		not specified	Uncertain significance (Oct 22, 2021)
19-51531196-C-T		not specified	Uncertain significance (Jan 22, 2024)
19-51531205-T-A		not specified	Uncertain significance (Sep 27, 2022)
19-51531268-T-C		not specified	Uncertain significance (Jan 03, 2024)
19-51531277-A-G		not specified	Uncertain significance (Dec 19, 2023)
19-51531295-C-A			Benign (Apr 01, 2023)
19-51531319-G-A		not specified	Uncertain significance (Apr 19, 2023)
19-51531439-G-A		not specified	Uncertain significance (Mar 20, 2023)
19-51531475-A-C		not specified	Uncertain significance (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIGLEC6	protein_coding	protein_coding	ENST00000425629	8	12332

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00588	0.990	125703	0	33	125736	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.242	249	260	0.958	0.0000142	2897
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000662	0.000641
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.000163	0.000163
South Asian	0.0000327	0.0000327
Other	0.000165	0.000163

dbNSFP

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

Recessive Scores

• pRec: 0.0710

Intolerance Scores

• loftool: 0.883
• rvis_EVS: 1.51
• rvis_percentile_EVS: 95.45

Haploinsufficiency Scores

• pHI: 0.0512
• hipred: N
• hipred_score: 0.154

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.177

Gene Damage Prediction

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

Gene ontology

• Biological process: cell adhesion;cell-cell signaling
• Cellular component: extracellular region;integral component of plasma membrane;membrane
• Molecular function: protein binding;carbohydrate binding