SELP

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

Basic information

Region (hg38): 1:169588849-169630193

Previous symbols: [ "GRMP" ]

Links

ENSG00000174175 ∙ NCBI:6403 ∙ OMIM:173610 ∙ HGNC:10721 ∙ Uniprot:P16109 ∙ 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 SELP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SELP 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	5	7
missense			42	4	7	53
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	43	6	12

Variants in SELP

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

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

Position	Type	Phenotype	Significance	ClinVar
1-169590158-G-A		not specified	Uncertain significance (Dec 13, 2023)
1-169590176-G-A		not specified	Uncertain significance (Jun 29, 2023)
1-169593647-C-A		not specified	Uncertain significance (Sep 14, 2022)
1-169593647-C-T		not specified	Uncertain significance (May 17, 2023)
1-169593660-A-C			Likely benign (Jun 23, 2018)
1-169593666-C-T		SELP-related disorder	Benign (Oct 21, 2019)
1-169593711-A-G			Benign (Jun 26, 2018)
1-169594707-C-A		not specified	Uncertain significance (Feb 05, 2024)
1-169594713-T-G		SELECTIN P POLYMORPHISM • SELP-related disorder	Benign (-)
1-169594856-T-G		not specified	Uncertain significance (Apr 25, 2022)
1-169594860-G-C		not specified	Uncertain significance (Jun 13, 2023)
1-169595955-G-T		not specified	Uncertain significance (Apr 25, 2022)
1-169595987-C-T		not specified	Uncertain significance (Jan 04, 2024)
1-169595990-A-G		not specified	Uncertain significance (Feb 28, 2023)
1-169596006-C-A		not specified	Uncertain significance (May 16, 2024)
1-169596006-C-T		not specified	Uncertain significance (Nov 09, 2021)
1-169596007-G-A			Likely benign (Apr 04, 2018)
1-169596008-T-C			Benign (Jul 13, 2018)
1-169596062-C-T		not specified	Uncertain significance (Sep 14, 2023)
1-169596104-T-C		not specified	Likely benign (Aug 01, 2022)
1-169596108-C-A		SELP-related disorder	Benign (Nov 06, 2019)
1-169596108-C-G		SELECTIN P POLYMORPHISM	Benign (Sep 01, 2003)
1-169597003-G-T			Uncertain significance (Mar 30, 2021)
1-169597027-A-C			Benign (Jul 13, 2018)
1-169597070-G-A		SELP-related disorder	Benign (Nov 06, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SELP	protein_coding	protein_coding	ENST00000263686	16	41345

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.04e-32	0.0000172	125156	4	588	125748	0.00236

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.256	474	459	1.03	0.0000239	5425
Missense in Polyphen		160	157.49	1.016		1910
Synonymous	-0.668	185	174	1.06	0.00000989	1564
Loss of Function	-0.215	47	45.4	1.03	0.00000209	544

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00165	0.00165
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000446	0.000435
Finnish	0.0122	0.0122
European (Non-Finnish)	0.00160	0.00159
Middle Eastern	0.000446	0.000435
South Asian	0.00401	0.00278
Other	0.00263	0.00245

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ca(2+)-dependent receptor for myeloid cells that binds to carbohydrates on neutrophils and monocytes. Mediates the interaction of activated endothelial cells or platelets with leukocytes. The ligand recognized is sialyl-Lewis X. Mediates rapid rolling of leukocyte rolling over vascular surfaces during the initial steps in inflammation through interaction with SELPLG. {ECO:0000269|PubMed:11081633, ECO:0000269|PubMed:28011641, ECO:0000269|PubMed:7585950}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Malaria - Homo sapiens (human);Staphylococcus aureus infection - Homo sapiens (human);Spinal Cord Injury;Human Complement System;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Cell surface interactions at the vascular wall;Hemostasis;amb2 Integrin signaling;IL4-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.530

Intolerance Scores

• loftool: 0.937
• rvis_EVS: 1.01
• rvis_percentile_EVS: 90.81

Haploinsufficiency Scores

• pHI: 0.0586
• hipred: N
• hipred_score: 0.146
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.537

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Selp
• Phenotype: growth/size/body region 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); homeostasis/metabolism phenotype; cellular phenotype; vision/eye phenotype; hematopoietic system phenotype; 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); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; renal/urinary system phenotype

Zebrafish Information Network

• Gene name: selp
• Affected structure: intermediate cell mass of mesoderm
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: platelet degranulation;positive regulation of leukocyte migration;inflammatory response;cell adhesion;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;leukocyte cell-cell adhesion;positive regulation of platelet activation;positive regulation of phosphatidylinositol 3-kinase signaling;calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules;response to lipopolysaccharide;regulation of integrin activation;calcium-mediated signaling using intracellular calcium source;defense response to Gram-negative bacterium;leukocyte migration;leukocyte tethering or rolling
• Cellular component: extracellular space;plasma membrane;integral component of plasma membrane;external side of plasma membrane;platelet dense granule membrane;platelet alpha granule membrane
• Molecular function: lipopolysaccharide binding;calcium ion binding;protein binding;heparin binding;sialic acid binding;fucose binding;glycosphingolipid binding;calcium-dependent protein binding;oligosaccharide binding