SLAMF9

SLAM family member 9, the group of V-set domain containing

Basic information

Region (hg38): 1:159951491-159954237

Links

ENSG00000162723 ∙ NCBI:89886 ∙ OMIM:608589 ∙ HGNC:18430 ∙ Uniprot:Q96A28 ∙ 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 SLAMF9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLAMF9 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				1	2	3
missense			8	3	4	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	4	6

Variants in SLAMF9

This is a list of pathogenic ClinVar variants found in the SLAMF9 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-159951686-G-T		not specified	Uncertain significance (Dec 06, 2023)
1-159951692-T-C		not specified	Uncertain significance (Jan 16, 2024)
1-159951697-C-A		not specified	Uncertain significance (Dec 19, 2023)
1-159951755-A-C		not specified	Uncertain significance (Sep 06, 2022)
1-159951805-G-A		not specified	Likely benign (Feb 06, 2024)
1-159951857-T-G		not specified	Uncertain significance (Nov 09, 2023)
1-159952280-C-T		not specified	Uncertain significance (Mar 20, 2024)
1-159952318-T-C		not specified	Likely benign (Dec 17, 2023)
1-159952385-C-T			Benign (Dec 31, 2019)
1-159952402-C-A		not specified	Uncertain significance (Mar 28, 2024)
1-159952412-G-A		not specified	Likely benign (Feb 10, 2022)
1-159952436-C-G			Benign (Aug 20, 2018)
1-159952463-C-T		not specified	Uncertain significance (Mar 02, 2023)
1-159952471-A-G		not specified	Uncertain significance (May 26, 2023)
1-159952473-A-G			Benign (Jun 27, 2018)
1-159953444-C-T			Benign (Jul 13, 2018)
1-159953446-T-C		not specified	Likely benign (Dec 21, 2021)
1-159953474-T-C		not specified	Uncertain significance (Mar 07, 2024)
1-159953605-G-A			Benign (Dec 31, 2019)
1-159953619-G-A			Benign (Jul 31, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLAMF9	protein_coding	protein_coding	ENST00000368093	4	2763

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000123	0.620	125717	0	29	125746	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.113	157	153	1.03	0.00000706	1897
Missense in Polyphen		36	38.046	0.94623		549
Synonymous	-0.923	67	58.1	1.15	0.00000278	561
Loss of Function	0.868	9	12.3	0.733	7.11e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000660	0.000660
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000448	0.0000439
Middle Eastern	0.000109	0.000109
South Asian	0.000133	0.000131
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the immune response. {ECO:0000269|PubMed:11300479}.

Recessive Scores

• pRec: 0.0635

Intolerance Scores

• loftool: 0.738
• rvis_EVS: 0.82
• rvis_percentile_EVS: 87.95

Haploinsufficiency Scores

• pHI: 0.0239
• hipred: N
• hipred_score: 0.132

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0519

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slamf9

Gene ontology

• Biological process: biological_process
• Cellular component: integral component of membrane
• Molecular function: molecular_function