FCRL2

Chr 1

Fc receptor like 2

Also known as: CD307b, FCRH2, IFGP4, IRTA4, SPAP1, SPAP1A, SPAP1B, SPAP1C

NCBI Gene: 79368 ENSG00000132704 UniProt: Q6BAA4 OMIM: 606509

This gene encodes a member of the immunoglobulin receptor superfamily and is one of several Fc receptor-like glycoproteins clustered on the long arm of chromosome 1. The encoded protein has four extracellular C2-type immunoglobulin domains, a transmembrane domain and a cytoplasmic domain that contains one immunoreceptor-tyrosine activation motif and two immunoreceptor-tyrosine inhibitory motifs. This protein may be a prognostic marker for chronic lymphocytic leukemia. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Apr 2009]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.12

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.12LOEUF

pLI 0.000

Z-score 1.08

OE 0.77 (0.54–1.12)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.48Z-score

OE missense 1.08 (0.98–1.19)

290 obs / 267.9 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.77 (0.54–1.12)

0≤0.351.4

Missense OE?1.08 (0.98–1.19)

0≤0.61.4

Synonymous OE?1.11

0≤1.21.6

LoF obs/exp: 20 / 25.9Missense obs/exp: 290 / 267.9Syn Z: -0.87

Background carrier burden — how many people carry a rare variant somewhere in FCRL2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 67

769 rare PASS variants

Rare truncating (LoF)

1 in 530

127 rare PASS variants

Rare synonymous (reference)

1 in 260

294 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for FCRL2. 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 76	1 in 1,600
South Asian	~43k	1 in 74	1 in 330
Remaining (unassigned)	~30k	1 in 60	1 in 200
European (Finnish)	~27k	1 in 130	≈ 1 in 13,000
Admixed American	~22k	1 in 61	1 in 590
African / African American	~21k	1 in 66	1 in 550
East Asian	~20k	1 in 100	1 in 440
Ashkenazi Jewish	~13k	1 in 280	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 96	1 in 220

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