SLAMF9

Chr 1

SLAM family member 9

Also known as: CD2F-10, CD2F10, CD84-H1, CD84H1, SF2001

NCBI Gene: 89886 ENSG00000162723 UniProt: Q96A28 OMIM: 608589

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]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.28

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.28LOEUF

pLI 0.000

Z-score 0.87

OE 0.73 (0.44–1.28)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.11Z-score

OE missense 1.03 (0.90–1.17)

157 obs / 153.1 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.73 (0.44–1.28)

0≤0.351.4

Missense OE?1.03 (0.90–1.17)

0≤0.61.4

Synonymous OE?1.15

0≤1.21.6

LoF obs/exp: 9 / 12.3Missense obs/exp: 157 / 153.1Syn Z: -0.92

Background carrier burden — how many people carry a rare variant somewhere in SLAMF9?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 150

374 rare PASS variants

Rare truncating (LoF)

1 in 1,900

64 rare PASS variants

Rare synonymous (reference)

1 in 240

142 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SLAMF9. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 250	1 in 2,200
South Asian	~43k	1 in 120	1 in 600
Remaining (unassigned)	~30k	1 in 120	1 in 2,300
European (Finnish)	~27k	1 in 500	≈ 1 in 13,000
Admixed American	~22k	1 in 220	1 in 1,200
African / African American	~21k	1 in 140	1 in 1,100
East Asian	~20k	1 in 130	1 in 1,200
Ashkenazi Jewish	~13k	≈ 1 in 6,500	none seen
Middle Eastern	~2,884	1 in 360	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 4 coding exons well covered in gnomAD exomes and genomes.? see exons ↓