CD84

Chr 1

CD84 molecule

Also known as: LY9B, SLAMF5, hCD84, mCD84

NCBI Gene: 8832 ENSG00000066294 UniProt: Q9UIB8 OMIM: 604513

This gene encodes a membrane glycoprotein that is a member of the signaling lymphocyte activation molecule (SLAM) family. This family forms a subset of the larger CD2 cell-surface receptor Ig superfamily. The encoded protein is a homophilic adhesion molecule that is expressed in numerous immune cells types and is involved in regulating receptor-mediated signaling in those cells. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2011]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.32

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.32LOEUF

pLI 0.000

Z-score 0.59

OE 0.84 (0.56–1.32)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.22Z-score

OE missense 0.96 (0.85–1.08)

184 obs / 192.4 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.84 (0.56–1.32)

0≤0.351.4

Missense OE?0.96 (0.85–1.08)

0≤0.61.4

Synonymous OE?1.04

0≤1.21.6

LoF obs/exp: 14 / 16.6Missense obs/exp: 184 / 192.4Syn Z: -0.27

Background carrier burden — how many people carry a rare variant somewhere in CD84?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 110

455 rare PASS variants

Rare truncating (LoF)

1 in 720

65 rare PASS variants

Rare synonymous (reference)

1 in 400

153 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for CD84. 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 140	1 in 680
South Asian	~43k	1 in 100	1 in 630
Remaining (unassigned)	~30k	1 in 91	1 in 1,000
European (Finnish)	~27k	1 in 700	1 in 760
Admixed American	~22k	1 in 99	1 in 1,600
African / African American	~21k	1 in 110	1 in 2,200
East Asian	~20k	1 in 160	1 in 950
Ashkenazi Jewish	~13k	1 in 1,600	none seen
Middle Eastern	~2,884	1 in 130	≈ 1 in 1,400

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 7 coding exons well covered in gnomAD exomes and genomes.? see exons ↓