SLAMF1

protein-coding

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

Gene summary

Enables SH2 domain binding activity; identical protein binding activity; and virus receptor activity. Involved in several processes, including negative regulation of CD40 signaling pathway; negative regulation of cytokine production; and positive regulation of MAPK cascade. Located in extracellular exosome. Is active in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:
  • SLAM

MANE transcript

NM_003037.5

Inheritance

—

ClinVar variants

U:21B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.41

Max pathogenic AF

—

Genomic locus

chr1:160,608,106-160,647,044

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~38.9 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLAMF1 variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 19
not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003037.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
0
missense
19
clinvar
2
clinvar
2
clinvar
23
nonsense
1
clinvar
1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total00212225
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_003037.5RefSeqNP_003028.17MANE Select
ENST00000302035.11EnsemblENSP00000306190.67MANE Select
NM_001330754.2RefSeqNP_001317683.18Standard
ENST00000538290.2EnsemblENSP00000438406.28Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Measles - Homo sapiens (human)

Biological Process

  • adaptive immune response
  • myeloid dendritic cell activation involved in immune response
  • phagocytosis
  • cell adhesion
  • positive regulation of cell population proliferation

Molecular Function

  • virus receptor activity
  • antigen binding
  • transmembrane signaling receptor activity
  • protein binding
  • identical protein binding

Cellular Component

  • plasma membrane
  • cell surface
  • integral component of membrane
  • extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000302035
Coding exons
7
Length
39196
Individuals with no LoFs
125727
Homozygous LoFs
0
Heterozygous LoFs
10
Defined
125737
p
0.0000398
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.6611651910.8650.00001032179
Missense (PolyPhen)2047.3850.42207604
Synonymous0.1467374.60.9780.00000416664
Loss of Function2.12614.80.4056.28e-7184

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish0.000230.00023rare
European (Non-Finnish)0.0000360.000035rare
South Asian0.0000330.000033rare
Other00.0absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec
0.246

Intolerance Scores

LoFtool
0.478
RVIS EVS
0.73
RVIS percentile EVS
86.17

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.741

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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