SIGLEC12

sialic acid binding Ig like lectin 12, the group of V-set domain containing|C2-set domain containing|Sialic acid binding Ig like lectins|I-set domain containing

Basic information

Region (hg38): 19:51491226-51501800

Previous symbols: [ "SIGLECL1" ]

Links

ENSG00000254521 ∙ NCBI:89858 ∙ OMIM:606094 ∙ HGNC:15482 ∙ Uniprot:Q96PQ1 ∙ 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 SIGLEC12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIGLEC12 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	2	3
missense			52	1		53
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	2	3

Variants in SIGLEC12

This is a list of pathogenic ClinVar variants found in the SIGLEC12 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-51491682-C-A		not specified	Uncertain significance (May 01, 2024)
19-51491788-G-T		not specified	Uncertain significance (Mar 15, 2024)
19-51491792-G-A		not specified	Uncertain significance (Jan 02, 2024)
19-51491823-G-T		not specified	Uncertain significance (Dec 20, 2021)
19-51491828-C-A		not specified	Uncertain significance (Jan 02, 2024)
19-51496902-G-A		not specified	Uncertain significance (Aug 16, 2022)
19-51496903-C-T		not specified	Uncertain significance (Aug 31, 2022)
19-51496909-C-T		not specified	Uncertain significance (Jul 21, 2021)
19-51496916-C-T		not specified	Uncertain significance (Mar 08, 2024)
19-51496927-C-T		not specified	Uncertain significance (Dec 11, 2023)
19-51496933-C-A		not specified	Uncertain significance (Apr 12, 2023)
19-51496969-A-G		not specified	Uncertain significance (Jun 02, 2023)
19-51496971-C-T		not specified	Uncertain significance (Feb 15, 2023)
19-51497366-G-C		not specified	Uncertain significance (Jun 17, 2022)
19-51497379-A-G		not specified	Uncertain significance (Feb 06, 2024)
19-51497388-G-A		not specified	Uncertain significance (Jan 23, 2023)
19-51497412-C-T		not specified	Uncertain significance (Oct 22, 2021)
19-51498062-G-A		not specified	Uncertain significance (Dec 20, 2021)
19-51498073-G-T		not specified	Uncertain significance (Feb 05, 2024)
19-51498083-C-T		not specified	Uncertain significance (Nov 15, 2021)
19-51498114-G-A		not specified	Uncertain significance (Jul 20, 2022)
19-51498143-T-C		not specified	Uncertain significance (Jan 24, 2024)
19-51498159-G-A		not specified	Uncertain significance (May 16, 2022)
19-51498215-A-G		not specified	Uncertain significance (Apr 14, 2022)
19-51498218-G-A		not specified	Likely benign (Dec 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIGLEC12	protein_coding	protein_coding	ENST00000291707	8	10433

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.22e-13	0.0858	125673	0	75	125748	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.673	363	329	1.10	0.0000173	3801
Missense in Polyphen		95	96.129	0.98826		1211
Synonymous	-2.05	177	146	1.22	0.00000851	1253
Loss of Function	0.661	22	25.6	0.859	0.00000154	247

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00169	0.00169
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000285	0.000281
Middle Eastern	0.000163	0.000163
South Asian	0.000241	0.000229
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative adhesion molecule that mediates sialic-acid dependent binding to cells. 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)

Intolerance Scores

• loftool: 0.945
• rvis_EVS: 2.34
• rvis_percentile_EVS: 98.4

Haploinsufficiency Scores

• pHI: 0.0634
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

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

Gene ontology

• Biological process: cell adhesion
• Cellular component: integral component of membrane
• Molecular function: carbohydrate binding