SIGLEC14

sialic acid binding Ig like lectin 14, the group of V-set domain containing|Sialic acid binding Ig like lectins

Basic information

Region (hg38): 19:51639478-51646825

Links

ENSG00000254415 ∙ NCBI:100049587 ∙ OMIM:618132 ∙ HGNC:32926 ∙ Uniprot:Q08ET2 ∙ 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 SIGLEC14 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIGLEC14 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	1

Variants in SIGLEC14

This is a list of pathogenic ClinVar variants found in the SIGLEC14 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-51643372-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)
19-51645823-G-A		not specified	Uncertain significance (May 23, 2024)
19-51645898-G-A		not specified	Uncertain significance (Oct 12, 2022)
19-51645913-G-T		not specified	Uncertain significance (Feb 22, 2023)
19-51645917-C-T		not specified	Uncertain significance (Apr 07, 2023)
19-51645938-C-G		not specified	Uncertain significance (May 17, 2023)
19-51645967-G-A			Likely benign (Mar 01, 2023)
19-51646004-T-C		not specified	Uncertain significance (Dec 21, 2022)
19-51646347-C-G		not specified	Uncertain significance (Dec 13, 2021)
19-51646425-C-G		not specified	Uncertain significance (Jan 16, 2024)
19-51646440-T-C		not specified	Uncertain significance (Jun 09, 2022)
19-51646488-C-G		not specified	Uncertain significance (Dec 09, 2023)
19-51646612-C-A		not specified	Uncertain significance (Aug 30, 2021)
19-51646726-C-G		not specified	Uncertain significance (Jun 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIGLEC14	protein_coding	protein_coding	ENST00000360844	7	4249

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00134	0.966	117180	2	21	117203	0.0000981

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.436	173	190	0.911	0.0000105	2499
Missense in Polyphen		43	48.69	0.88315		731
Synonymous	2.28	55	81.1	0.678	0.00000463	831
Loss of Function	1.88	7	14.8	0.472	7.06e-7	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000238	0.000238
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000194	0.0000182
Middle Eastern	0.00	0.00
South Asian	0.000568	0.000462
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative adhesion molecule. Sialic acid-binding paired receptor which may activate associated receptors. {ECO:0000269|PubMed:17012248}.
• Pathway: Neutrophil degranulation;DAP12 interactions;Innate Immune System;Immune System (Consensus)

Haploinsufficiency Scores

• pHI: 0.0586
• hipred: N
• hipred_score: 0.218
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0332

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;neutrophil degranulation;innate immune response
• Cellular component: plasma membrane;integral component of membrane;tertiary granule membrane;ficolin-1-rich granule membrane
• Molecular function: carbohydrate binding