SPN

sialophorin, the group of CD molecules

Basic information

Region (hg38): 16:29662978-29670876

Links

ENSG00000197471 ∙ ∙ OMIM:182160 ∙ HGNC:11249 ∙ Uniprot:P16150 ∙ 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 SPN gene.

• Inborn genetic diseases (19 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPN 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					3	3
missense			17	2	3	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	2	6

Variants in SPN

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

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

Position	Type	Phenotype	Significance	ClinVar
16-29663755-G-T		SPN-related disorder	Likely benign (Apr 25, 2019)
16-29663770-C-A		not specified	Uncertain significance (Sep 13, 2023)
16-29663793-C-T		SPN-related disorder	Benign (Mar 03, 2020)
16-29663921-C-G		not specified	Uncertain significance (Jan 10, 2023)
16-29663985-G-A		not specified	Uncertain significance (Feb 15, 2023)
16-29664005-A-G		SPN-related disorder	Benign (May 23, 2019)
16-29664050-G-A		not specified	Uncertain significance (Jan 26, 2023)
16-29664115-C-G		SPN-related disorder	Likely benign (Apr 20, 2023)
16-29664152-A-G		not specified	Uncertain significance (Feb 22, 2023)
16-29664186-C-T		not specified	Likely benign (Aug 30, 2021)
16-29664202-G-A		SPN-related disorder	Likely benign (Mar 22, 2019)
16-29664210-C-T		not specified	Uncertain significance (Feb 28, 2023)
16-29664354-C-T		not specified	Uncertain significance (Dec 07, 2021)
16-29664376-C-T		SPN-related disorder	Benign (Apr 10, 2019)
16-29664380-G-A		not specified	Likely benign (Jan 23, 2024)
16-29664394-G-C		not specified	Uncertain significance (Aug 02, 2021)
16-29664403-C-G		SPN-related disorder	Likely benign (Feb 07, 2022)
16-29664403-C-T			Benign (May 16, 2018)
16-29664420-T-C		not specified	Uncertain significance (Jul 21, 2021)
16-29664525-C-T			Benign (Jul 31, 2018)
16-29664565-G-A			Benign (Aug 20, 2018)
16-29664579-G-A		not specified	Uncertain significance (Dec 21, 2022)
16-29664607-C-T		SPN-related disorder	Benign (Oct 21, 2019)
16-29664608-G-A		not specified	Uncertain significance (Sep 13, 2023)
16-29664620-G-C		not specified	Uncertain significance (Aug 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPN	protein_coding	protein_coding	ENST00000360121	1	7888

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0144	0.462	125665	0	4	125669	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0855	228	224	1.02	0.0000133	2471
Missense in Polyphen		75	59.09	1.2692		600
Synonymous	-0.402	99	94.0	1.05	0.00000577	978
Loss of Function	-0.796	2	1.10	1.82	1.46e-7	3

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00000883	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Predominant cell surface sialoprotein of leukocytes which regulates multiple T-cell functions, including T-cell activation, proliferation, differentiation, trafficking and migration. Positively regulates T-cell trafficking to lymph-nodes via its association with ERM proteins (EZR, RDX and MSN) (By similarity). Negatively regulates Th2 cell differentiation and predisposes the differentiation of T-cells towards a Th1 lineage commitment. Promotes the expression of IFN-gamma by T-cells during T-cell receptor (TCR) activation of naive cells and induces the expression of IFN-gamma by CD4(+) T-cells and to a lesser extent by CD8(+) T-cells (PubMed:18036228). Plays a role in preparing T- cells for cytokine sensing and differentiation into effector cells by inducing the expression of cytokine receptors IFNGR and IL4R, promoting IFNGR and IL4R signaling and by mediating the clustering of IFNGR with TCR (PubMed:24328034). Acts as a major E-selectin ligand responsible for Th17 cell rolling on activated vasculature and recruitment during inflammation. Mediates Th17 cells, but not Th1 cells, adhesion to E-selectin. Acts as a T-cell counter- receptor for SIGLEC1 (By similarity). {ECO:0000250|UniProtKB:P15702, ECO:0000269|PubMed:18036228, ECO:0000269|PubMed:24328034}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Cell surface interactions at the vascular wall;Hemostasis;Basigin interactions (Consensus)

Recessive Scores

• pRec: 0.495

Intolerance Scores

• loftool: 0.595
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.6

Haploinsufficiency Scores

• pHI: 0.348
• hipred: N
• hipred_score: 0.182
• ghis: 0.637

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.835

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spn
• Phenotype: immune system phenotype; hematopoietic system phenotype; neoplasm

Gene ontology

• Biological process: T-helper 1 cell lineage commitment;chemotaxis;immune response;cellular defense response;negative regulation of cell adhesion;establishment or maintenance of cell polarity;signal transduction;interferon-gamma production;negative regulation of T cell proliferation;positive regulation of tumor necrosis factor biosynthetic process;defense response to bacterium;leukocyte migration;leukocyte tethering or rolling;regulation of T cell migration;positive regulation of T cell migration
• Cellular component: uropod;extracellular space;plasma membrane;integral component of plasma membrane;microvillus;cell surface;membrane;PML body;extracellular exosome
• Molecular function: transmembrane signaling receptor activity;Hsp70 protein binding;heat shock protein binding