SLAMF8

protein-coding

SLAM family member 8, the group of Immunoglobulin like domain containing|CD molecules

Gene summary

This gene encodes a member of the CD2 family of cell surface proteins involved in lymphocyte activation. These proteins are characterized by Ig domains. This protein is expressed in lymphoid tissues, and studies of a similar protein in mouse suggest that it may function during B cell lineage commitment. The gene is found in a region of chromosome 1 containing many CD2 genes. [provided by RefSeq, Jul 2008]

MANE transcript

NM_020125.3

Inheritance

—

ClinVar variants

U:48B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.7

Max pathogenic AF

—

Genomic locus

chr1:159,826,811-159,837,492

External References & Databases

Ensembl (ENSG00000158714)

Transcript & Mutation Effects

hg38 • Region Span ~10.7 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 SLAMF8 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 46

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020125.3. 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			1 clinvar			1
missense			46 clinvar	4 clinvar		50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	48	4	0	52

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020125.3	RefSeq	NP_064510.1	5	MANE Select
ENST00000289707.10	Ensembl	ENSP00000289707.5	5	MANE Select
NM_001330741.2	RefSeq	NP_001317670.1	4	Standard
ENST00000368104.4	Ensembl	ENSP00000357084.4	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

leukocyte chemotaxis involved in inflammatory response
B-1 B cell lineage commitment
negative regulation of macrophage chemotaxis
regulation of NAD(P)H oxidase activity
cellular response to drug

Molecular Function

signaling receptor activity
identical protein binding

Cellular Component

cell surface
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000289707
Coding exons: 5
Length: 10500
Individuals with no LoFs: 124763
Homozygous LoFs: 24
Heterozygous LoFs: 961
Defined: 125748
p: 0.00392

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.289	172	162	1.06	0.00000880	1825
Missense (PolyPhen)		21	30.078	0.69819		370
Synonymous	0.309	66	69.3	0.953	0.00000404	609
Loss of Function	1.04	10	14.2	0.704	8.66e-7	120

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00095	0.00095	rare
Ashkenazi Jewish	0.0024	0.0023	notable
East Asian	0.044	0.044	notable
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00085	0.00085	rare
South Asian	0.00069	0.00069	rare
Other	0.0029	0.0029	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in B-lineage commitment and/or modulation of signaling through the B-cell receptor. {ECO:0000269|PubMed:11313408}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.932
RVIS EVS: 0
RVIS percentile EVS: 53.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.185

Gene Damage Prediction

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