SLAMF9

protein-coding

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

Gene summary

This gene encodes a member of the signaling lymphocytic activation molecule family. The encoded protein is a cell surface molecule that consists of two extracellular immunoglobulin domains, a transmembrane domain and a short cytoplasmic tail that lacks the signal transduction motifs found in other family members. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Apr 2009]

MANE transcript

NM_033438.4

Inheritance

—

ClinVar variants

U:40B:13

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.73

Max pathogenic AF

—

Genomic locus

chr1:159,951,492-159,954,237

External References & Databases

Ensembl (ENSG00000162723)

Transcript & Mutation Effects

hg38 • Region Span ~2.7 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 SLAMF9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 41

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033438.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar	2 clinvar	5
missense			37 clinvar	4 clinvar	4 clinvar	45
nonsense						0
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	40	7	6	53

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033438.4	RefSeq	NP_254273.2	4	MANE Select
ENST00000368093.4	Ensembl	ENSP00000357072.3	4	MANE Select
NM_001146172.2	RefSeq	NP_001139644.1	3	Standard
NM_001146173.2	RefSeq	NP_001139645.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

molecular_function

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368093
Coding exons: 4
Length: 2763
Individuals with no LoFs: 125717
Homozygous LoFs: 0
Heterozygous LoFs: 29
Defined: 125746
p: 0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.113	157	153	1.03	0.00000706	1897
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000045	0.000044	rare
South Asian	0.00013	0.00013	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0519

Gene Damage Prediction

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