SLAMF1

signaling lymphocytic activation molecule family member 1, the group of Immunoglobulin like domain containing|CD molecules|Ig-like cell adhesion molecule family

Basic information

Region (hg38): 1:160608105-160647044

Previous symbols: [ "SLAM" ]

Links

ENSG00000117090 ∙ NCBI:6504 ∙ OMIM:603492 ∙ HGNC:10903 ∙ Uniprot:Q13291 ∙ 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 SLAMF1 gene.

• Inborn genetic diseases (5 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLAMF1 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						0
missense			4	1	2	7
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	1	2

Variants in SLAMF1

This is a list of pathogenic ClinVar variants found in the SLAMF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-160612502-G-A			Benign (Nov 20, 2018)
1-160612522-A-G		not specified	Uncertain significance (Apr 08, 2022)
1-160612529-T-C			Benign (Dec 31, 2019)
1-160612534-G-A		not specified	Uncertain significance (Nov 02, 2023)
1-160612541-G-C		not specified	Uncertain significance (Jan 29, 2024)
1-160619843-G-A		not specified	Uncertain significance (Apr 18, 2023)
1-160634624-G-A		not specified	Uncertain significance (Feb 17, 2022)
1-160634627-C-T		not specified	Uncertain significance (Nov 08, 2022)
1-160634729-G-A		not specified	Uncertain significance (Aug 09, 2021)
1-160637308-G-T		not specified	Uncertain significance (Nov 09, 2023)
1-160637394-T-C			Likely benign (Mar 29, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLAMF1	protein_coding	protein_coding	ENST00000302035	7	39196

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00704	0.978	125727	0	10	125737	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.661	165	191	0.865	0.0000103	2179
Missense in Polyphen		20	47.385	0.42207		604
Synonymous	0.146	73	74.6	0.978	0.00000416	664
Loss of Function	2.12	6	14.8	0.405	6.28e-7	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000231	0.000231
European (Non-Finnish)	0.0000359	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Self-ligand receptor of the signaling lymphocytic activation molecule (SLAM) family. SLAM receptors triggered by homo- or heterotypic cell-cell interactions are modulating the activation and differentiation of a wide variety of immune cells and thus are involved in the regulation and interconnection of both innate and adaptive immune response. Activities are controlled by presence or absence of small cytoplasmic adapter proteins, SH2D1A/SAP and/or SH2D1B/EAT-2. SLAMF1-induced signal- transduction events in T-lymphocytes are different from those in B-cells. Two modes of SLAMF1 signaling seem to exist: one depending on SH2D1A (and perhaps SH2D1B) and another in which protein-tyrosine phosphatase 2C (PTPN11)-dependent signal transduction operates. Initially it has been proposed that association with SH2D1A prevents binding to inhibitory effectors including INPP5D/SHIP1 and PTPN11/SHP-2 (PubMed:11806999). However, signaling is also regulated by SH2D1A which can simultaneously interact with and recruit FYN which subsequently phosphorylates and activates SLAMF1 (PubMed:12458214). Mediates IL-2-independent proliferation of activated T-cells during immune responses and induces IFN-gamma production (By similarity). Downstreaming signaling involves INPP5D, DOK1 and DOK2 leading to inhibited IFN-gamma production in T-cells, and PRKCQ, BCL10 and NFKB1 leading to increased T-cell activation and Th2 cytokine production (By similarity). Promotes T-cell receptor-induced IL-4 secretion by CD4(+) cells (By similarity). Inhibits antigen receptor-mediated production of IFN-gamma, but not IL-2, in CD4(-)/CD8(-) T-cells (By similarity). Required for IL-4 production by germinal centers T follicular helper (T(Fh))cells (By similarity). May inhibit CD40-induced signal transduction in monocyte-derived dendritic cells (PubMed:16317102). May play a role in allergic responses and may regulate allergen-induced Th2 cytokine and Th1 cytokine secretion (By similarity). In conjunction with SLAMF6 controls the transition between positive selection and the subsequent expansion and differentiation of the thymocytic natural killer T (NKT) cell lineage. Involved in the peripheral differentiation of indifferent natural killer T (iNKT) cells toward a regulatory NKT2 type (By similarity). In macrophages involved in down-regulation of IL-12, TNF-alpha and nitric oxide in response to lipopolysaccharide (LPS) (By similarity). In B-cells activates the ERK signaling pathway independently of SH2D1A but implicating both, SYK and INPP5D, and activates Akt signaling dependent on SYK and SH2D1A (By similarity). In B-cells also activates p38 MAPK and JNK1 and JNK2 (PubMed:20231852). In conjunction with CD84/SLAMF5 and SLAMF6 may be a negative regulator of the humoral immune response (By similarity). Involved in innate immune response against Gram- negative bacteria in macrophages; probably recognizes OmpC and/or OmpF on the bacterial surface, regulates phagosome maturation and recruitment of the PI3K complex II (PI3KC3-C2) leading to accumulation of PdtIns(3)P and NOX2 activity in the phagosomes (PubMed:20818396). {ECO:0000250|UniProtKB:Q9QUM4, ECO:0000269|PubMed:16317102, ECO:0000269|PubMed:20231852, ECO:0000269|PubMed:20818396, ECO:0000305|PubMed:11806999, ECO:0000305|PubMed:12458214}.
• Pathway: Measles - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.246

Intolerance Scores

• loftool: 0.478
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.17

Haploinsufficiency Scores

• pHI: 0.0997
• hipred: Y
• hipred_score: 0.508
• ghis: 0.446

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.741

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slamf1
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: adaptive immune response;myeloid dendritic cell activation involved in immune response;phagocytosis;cell adhesion;positive regulation of cell population proliferation;negative regulation of interleukin-12 production;negative regulation of interleukin-6 production;negative regulation of tumor necrosis factor production;innate immune response;positive regulation of JNK cascade;lymphocyte activation;viral entry into host cell;positive regulation of ERK1 and ERK2 cascade;negative regulation of CD40 signaling pathway
• Cellular component: plasma membrane;cell surface;integral component of membrane;extracellular exosome
• Molecular function: virus receptor activity;antigen binding;transmembrane signaling receptor activity;protein binding;identical protein binding