SLAMF6
SLAM family member 6, the group of V-set domain containing|CD molecules|Ig-like cell adhesion molecule family
Basic information
Region (hg38): 1:160485030-160523262
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLAMF6 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 | 10 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 2 | 0 |
Variants in SLAMF6
This is a list of pathogenic ClinVar variants found in the SLAMF6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-160486712-C-T | not specified | Uncertain significance (Jun 21, 2023) | ||
| 1-160486729-G-A | not specified | Uncertain significance (Sep 20, 2023) | ||
| 1-160486744-G-A | not specified | Likely benign (Jan 30, 2024) | ||
| 1-160487167-T-A | not specified | Uncertain significance (Aug 09, 2021) | ||
| 1-160490604-A-G | not specified | Uncertain significance (Jul 26, 2022) | ||
| 1-160490617-C-T | not specified | Uncertain significance (Jan 26, 2023) | ||
| 1-160490647-A-G | not specified | Uncertain significance (Jan 04, 2024) | ||
| 1-160490650-G-T | not specified | Uncertain significance (Aug 03, 2022) | ||
| 1-160491128-C-T | not specified | Likely benign (Mar 07, 2023) | ||
| 1-160491181-G-A | not specified | Uncertain significance (Dec 27, 2023) | ||
| 1-160491232-G-T | not specified | Uncertain significance (Mar 01, 2023) | ||
| 1-160496166-A-C | not specified | Uncertain significance (May 14, 2024) | ||
| 1-160496228-C-T | not specified | Uncertain significance (Mar 21, 2024) | ||
| 1-160496306-G-T | not specified | Uncertain significance (Apr 09, 2024) | ||
| 1-160496349-C-T | not specified | Uncertain significance (Jan 29, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLAMF6 | protein_coding | protein_coding | ENST00000368057 | 8 | 38233 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0187 | 0.978 | 125678 | 0 | 7 | 125685 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.571 | 148 | 169 | 0.876 | 0.00000818 | 2160 |
| Missense in Polyphen | 24 | 42.307 | 0.56728 | 607 | ||
| Synonymous | 0.896 | 58 | 67.4 | 0.861 | 0.00000359 | 657 |
| Loss of Function | 2.54 | 6 | 17.4 | 0.344 | 9.15e-7 | 190 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000549 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000353 | 0.0000352 |
| Middle Eastern | 0.0000549 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- 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. Triggers cytolytic activity only in natural killer cells (NK) expressing high surface densities of natural cytotoxicity receptors (PubMed:11489943, PubMed:16920955). Positive signaling in NK cells implicates phosphorylation of VAV1. NK cell activation seems to depend on SH2D1B and not on SH2D1A (PubMed:16920955). In conjunction with SLAMF1 controls the transition between positive selection and the subsequent expansion and differentiation of the thymocytic natural killer T (NKT) cell lineage (By similarity). Promotes T-cell differentiation into a helper T-cell Th17 phenotype leading to increased IL-17 secretion; the costimulatory activity requires SH2D1A (PubMed:22184727, PubMed:16920955). Promotes recruitment of RORC to the IL-17 promoter (PubMed:22989874). In conjunction with SLAMF1 and CD84/SLAMF5 may be a negative regulator of the humoral immune response. In the absence of SH2D1A/SAP can transmit negative signals to CD4(+) T-cells and NKT cells. Negatively regulates germinal center formation by inhibiting T-cell:B-cell adhesion; the function probably implicates increased association with PTPN6/SHP-1 via ITSMs in absence of SH2D1A/SAP. However, reported to be involved in maintaining B-cell tolerance in germinal centers and in preventing autoimmunity (By similarity). {ECO:0000250|UniProtKB:Q9ET39, ECO:0000269|PubMed:11489943, ECO:0000269|PubMed:16920955, ECO:0000269|PubMed:22184727, ECO:0000269|PubMed:22989874}.;
- Pathway
- TCR;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System
(Consensus)
Recessive Scores
- pRec
- 0.112
Intolerance Scores
- loftool
- 0.504
- rvis_EVS
- -0.43
- rvis_percentile_EVS
- 25.15
Haploinsufficiency Scores
- pHI
- 0.0267
- hipred
- Y
- hipred_score
- 0.519
- ghis
- 0.542
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.235
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slamf6
- Phenotype
- immune system phenotype; 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); normal phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- positive regulation of interferon-gamma production;positive regulation of interleukin-17 production;innate immune response;positive regulation of natural killer cell mediated cytotoxicity;regulation of immune response;T-helper 17 cell lineage commitment
- Cellular component
- plasma membrane;integral component of membrane;extracellular exosome
- Molecular function
- protein binding