SELL

selectin L, the group of C-type lectin domain containing|CD molecules|Sushi domain containing|Selectins

Basic information

Region (hg38): 1:169690664-169711702

Previous symbols: [ "LYAM1", "LNHR" ]

Links

ENSG00000188404 ∙ NCBI:6402 ∙ OMIM:153240 ∙ HGNC:10720 ∙ Uniprot:P14151 ∙ 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 SELL gene.

• Inborn genetic diseases (8 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SELL 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					2	2
missense			7	1	2	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	4

Variants in SELL

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

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

Position	Type	Phenotype	Significance	ClinVar
1-169701571-C-A		not specified	Uncertain significance (Jun 30, 2022)
1-169701668-T-C		not specified	Uncertain significance (Oct 14, 2023)
1-169701681-G-T		not specified	Uncertain significance (Jan 03, 2022)
1-169703321-T-G		not specified	Uncertain significance (Sep 07, 2022)
1-169703422-A-G		not specified	Uncertain significance (Dec 21, 2023)
1-169704603-A-G		not specified	Uncertain significance (Dec 16, 2023)
1-169704637-A-T		not specified	Uncertain significance (Nov 03, 2022)
1-169704686-G-C		not specified	Uncertain significance (Dec 28, 2023)
1-169704733-C-G			Benign (Apr 24, 2018)
1-169707344-A-T		not specified	Uncertain significance (Aug 16, 2021)
1-169707357-G-A		not specified	Uncertain significance (Dec 03, 2021)
1-169707371-A-G		not specified	Uncertain significance (Jan 12, 2024)
1-169707414-C-G		not specified	Uncertain significance (Jul 12, 2023)
1-169708538-A-G			Benign (Dec 31, 2019)
1-169708606-C-T		not specified	Uncertain significance (Jan 18, 2022)
1-169708716-C-T		not specified	Likely benign (Dec 01, 2022)
1-169708782-G-C			Benign (May 13, 2018)
1-169710455-C-A			Benign (Feb 16, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SELL	protein_coding	protein_coding	ENST00000236147	9	21032

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.96e-7	0.859	124602	0	17	124619	0.0000682

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.320	179	191	0.935	0.00000908	2514
Missense in Polyphen		56	74.001	0.75675		959
Synonymous	0.170	63	64.7	0.973	0.00000316	647
Loss of Function	1.53	13	20.5	0.635	8.64e-7	278

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000649	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000559	0.0000557
Finnish	0.00	0.00
European (Non-Finnish)	0.0000851	0.0000797
Middle Eastern	0.0000559	0.0000557
South Asian	0.000230	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-dependent lectin that mediates cell adhesion by binding to glycoproteins on neighboring cells (PubMed:12403782, PubMed:28489325, PubMed:28011641). Mediates the adherence of lymphocytes to endothelial cells of high endothelial venules in peripheral lymph nodes. Promotes initial tethering and rolling of leukocytes in endothelia (PubMed:12403782, PubMed:28011641). {ECO:0000269|PubMed:12403782, ECO:0000269|PubMed:28011641, ECO:0000305|PubMed:28489325}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Human Complement System;Neutrophil degranulation;Innate Immune System;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.564

Intolerance Scores

• rvis_EVS: 0.79
• rvis_percentile_EVS: 87.4

Haploinsufficiency Scores

• pHI: 0.258
• hipred: N
• hipred_score: 0.401
• ghis: 0.396

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.871

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sell
• Phenotype: endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; neoplasm; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; respiratory system phenotype; liver/biliary system phenotype; immune system phenotype

Gene ontology

• Biological process: cell adhesion;calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules;response to ATP;neutrophil degranulation;regulation of immune response;leukocyte migration;leukocyte tethering or rolling
• Cellular component: plasma membrane;integral component of plasma membrane;external side of plasma membrane;secretory granule membrane
• Molecular function: protease binding;calcium ion binding;protein binding;heparin binding;carbohydrate binding;glycosphingolipid binding;cell adhesion molecule binding;oligosaccharide binding