FCRL4

Fc receptor like 4, the group of CD molecules|Immunoglobulin like domain containing|Fc receptors

Basic information

Region (hg38): 1:157573747-157598085

Links

ENSG00000163518 ∙ NCBI:83417 ∙ OMIM:605876 ∙ HGNC:18507 ∙ Uniprot:Q96PJ5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FCRL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FCRL4 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			20	4	2	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	21	4	3

Variants in FCRL4

This is a list of pathogenic ClinVar variants found in the FCRL4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-157575528-C-T		not specified	Uncertain significance (Mar 31, 2024)
1-157575579-G-A		not specified	Uncertain significance (Apr 05, 2023)
1-157578512-G-C		not specified	Uncertain significance (May 23, 2023)
1-157578530-T-C		not specified	Uncertain significance (Oct 06, 2024)
1-157578533-T-C			Benign (Apr 04, 2018)
1-157578829-C-A		not specified	Uncertain significance (Sep 29, 2023)
1-157580329-G-C		not specified	Uncertain significance (Dec 14, 2023)
1-157580330-T-C		not specified	Uncertain significance (Aug 16, 2021)
1-157580339-A-G		not specified	Uncertain significance (Oct 20, 2023)
1-157580343-C-A		not specified	Uncertain significance (Jun 18, 2024)
1-157581559-C-G			Benign (Apr 04, 2018)
1-157586176-G-A		not specified	Uncertain significance (Jul 31, 2024)
1-157586180-C-T		not specified	Likely benign (Aug 22, 2023)
1-157586207-C-T		not specified	Uncertain significance (Apr 24, 2024)
1-157586219-C-T		not specified	Uncertain significance (Jul 14, 2024)
1-157586240-C-G		not specified	Uncertain significance (Jan 03, 2024)
1-157586257-A-T		not specified	Uncertain significance (May 24, 2023)
1-157586291-G-A		not specified	Uncertain significance (Feb 16, 2023)
1-157586294-G-C		not specified	Uncertain significance (Apr 24, 2024)
1-157586312-T-C		not specified	Uncertain significance (Oct 30, 2023)
1-157586363-C-T		not specified	Uncertain significance (Apr 07, 2023)
1-157586404-G-A		not specified	Likely benign (Feb 28, 2024)
1-157586414-C-G		not specified	Uncertain significance (Nov 10, 2024)
1-157586422-T-A		not specified	Uncertain significance (Oct 19, 2024)
1-157587275-C-T		Non-immune hydrops fetalis • not specified	Uncertain significance (Mar 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FCRL4	protein_coding	protein_coding	ENST00000271532	12	24332

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.91e-10	0.890	125673	0	73	125746	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.577	302	275	1.10	0.0000144	3281
Missense in Polyphen		67	77.581	0.86361		1011
Synonymous	0.399	106	111	0.952	0.00000605	1046
Loss of Function	1.81	19	29.6	0.642	0.00000161	314

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00104	0.00104
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000319	0.000316
Middle Eastern	0.000272	0.000272
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as an inhibitor of the B-cell receptor signaling. May function in the B-cell-mediated immune response. {ECO:0000269|PubMed:14597715}.
• Disease: DISEASE: Note=A chromosomal aberration involving FCRL4 is found in non-Hodgkin lymphoma (NHG). Translocation t(1;1)(p36.3; q21.1-2). {ECO:0000269|PubMed:12619161}.; DISEASE: Note=A chromosomal aberration involving FCRL4 is found in multiple myeloma (MM). Translocation t(1;14)(q21;q32) that forms a FCRL4-IGHA1 fusion protein. {ECO:0000269|PubMed:11290337}.

Recessive Scores

• pRec: 0.0856

Intolerance Scores

• loftool: 0.835
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.3

Haploinsufficiency Scores

• pHI: 0.0493
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0365

Gene Damage Prediction

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

Gene ontology

• Biological process: adaptive immune response
• Cellular component: plasma membrane;cell surface;integral component of membrane
• Molecular function: protein binding