SLAMF1

Chr 1

signaling lymphocytic activation molecule family member 1

Also known as: CD150, CDw150, IPO3, SLAM

NCBI Gene: 6504 ENSG00000117090 UniProt: Q13291 OMIM: 603492

Enables SH2 domain binding activity; identical protein binding activity; and virus receptor activity. Involved in several processes, including negative regulation of CD40 signaling pathway; negative regulation of cytokine production; and positive regulation of MAPK cascade. Located in extracellular exosome. Is active in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

MultiplemechanismLOEUF 0.80

Clinical Summary— SLAMF1

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Population Constraint (gnomAD)

Low constraint (pLI 0.01) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

18 VUS of 29 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.80LOEUF

pLI 0.007

Z-score 2.12

OE 0.41 (0.22–0.80)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.66Z-score

OE missense 0.87 (0.76–0.98)

165 obs / 190.7 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.41 (0.22–0.80)

0≤0.351.4

Missense OE?0.87 (0.76–0.98)

0≤0.61.4

Synonymous OE?0.98

0≤1.21.6

LoF obs/exp: 6 / 14.8Missense obs/exp: 165 / 190.7Syn Z: 0.15

This gene — mechanism propensity

0.75top 25%

GOF

0.76top 25%

LOF

0.2387th %ile

This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

GOFprediction above median

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

29 submitted variants in ClinVar

ClinVar

Classification Summary

VUS18

Likely Benign2

Benign2

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	1	17	18
Likely Benign	0	2	2
Benign	0	2	2
Total	1	21	22

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

11 pathogenic / likely-pathogenic (of 16) ClinVar copy-number / structural variants overlap SLAMF1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →