SLAMF7

SLAM family member 7, the group of V-set domain containing|CD molecules

Basic information

Region (hg38): 1:160739057-160754821

Links

ENSG00000026751 ∙ NCBI:57823 ∙ OMIM:606625 ∙ HGNC:21394 ∙ Uniprot:Q9NQ25 ∙ 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 SLAMF7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLAMF7 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			5	1	1	7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	1	1

Variants in SLAMF7

This is a list of pathogenic ClinVar variants found in the SLAMF7 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-160739350-C-A		not specified	Uncertain significance (Sep 08, 2024)
1-160748365-G-T		not specified	Uncertain significance (Aug 12, 2021)
1-160749926-T-C		not specified	Likely benign (Jun 12, 2023)
1-160749967-C-T			Benign (Dec 31, 2019)
1-160750382-T-G		not specified	Uncertain significance (Dec 04, 2024)
1-160750409-G-C		not specified	Uncertain significance (Apr 20, 2024)
1-160751371-G-A		not specified	Uncertain significance (Jul 14, 2021)
1-160751372-A-G		not specified	Uncertain significance (Jul 14, 2021)
1-160753110-A-C		not specified	Uncertain significance (Jun 30, 2023)
1-160753122-C-A		Autism	Uncertain significance (-)
1-160753125-T-G		not specified	Uncertain significance (Oct 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLAMF7	protein_coding	protein_coding	ENST00000368043	7	15575

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0364	0.957	125663	0	2	125665	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.941	146	182	0.804	0.00000896	2169
Missense in Polyphen		22	38.908	0.56544		529
Synonymous	-0.0545	74	73.4	1.01	0.00000391	676
Loss of Function	2.37	5	14.9	0.337	6.30e-7	180

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	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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. Isoform 1 mediates NK cell activation through a SH2D1A-independent extracellular signal- regulated ERK-mediated pathway (PubMed:11698418). Positively regulates NK cell functions by a mechanism dependent on phosphorylated SH2D1B. Downstream signaling implicates PLCG1, PLCG2 and PI3K (PubMed:16339536). In addition to heterotypic NK cells-target cells interactions also homotypic interactions between NK cells may contribute to activation. However, in the absence of SH2D1B, inhibits NK cell function. Acts also inhibitory in T-cells (By similarity). May play a role in lymphocyte adhesion (PubMed:11802771). In LPS-activated monocytes negatively regulates production of proinflammatory cytokines (PubMed:23695528). {ECO:0000250|UniProtKB:Q8BHK6, ECO:0000269|PubMed:11698418, ECO:0000269|PubMed:11802771, ECO:0000269|PubMed:16339536, ECO:0000269|PubMed:23695528, ECO:0000269|Ref.4}.
• Pathway: Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Fibroblast growth factor-1 (Consensus)

Recessive Scores

• pRec: 0.214

Intolerance Scores

• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.38

Haploinsufficiency Scores

• pHI: 0.0354
• hipred: N
• hipred_score: 0.139
• ghis: 0.469

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.164

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slamf7
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: adaptive immune response;cell adhesion;natural killer cell activation;natural killer cell mediated cytotoxicity;regulation of immune response
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: identical protein binding