FCRL5

Fc receptor like 5, the group of Fc receptors|Immunoglobulin like domain containing|CD molecules

Basic information

Region (hg38): 1:157513376-157552515

Links

ENSG00000143297 ∙ NCBI:83416 ∙ OMIM:605877 ∙ HGNC:18508 ∙ Uniprot:Q96RD9 ∙ 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 FCRL5 gene.

• Inborn genetic diseases (43 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FCRL5 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	3	4
missense			38	5	3	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	38	7	6

Variants in FCRL5

This is a list of pathogenic ClinVar variants found in the FCRL5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-157515636-G-C		not specified	Uncertain significance (Jan 08, 2024)
1-157515642-A-G		not specified	Likely benign (Dec 03, 2021)
1-157515721-G-A		not specified	Uncertain significance (Jan 23, 2024)
1-157518433-A-T		not specified	Uncertain significance (Oct 02, 2023)
1-157520500-C-T		not specified	Uncertain significance (Jul 11, 2023)
1-157520506-C-T		not specified	Likely benign (Mar 01, 2024)
1-157520519-A-C		not specified	Uncertain significance (May 24, 2023)
1-157520539-C-A		not specified	Uncertain significance (Nov 09, 2023)
1-157520545-G-T		not specified	Uncertain significance (Jan 26, 2023)
1-157521023-T-C		not specified	Uncertain significance (Dec 15, 2022)
1-157521067-T-C		not specified	Uncertain significance (May 31, 2023)
1-157521101-C-A		not specified	Uncertain significance (Mar 01, 2024)
1-157521241-G-A		not specified	Likely benign (Apr 06, 2022)
1-157521265-A-C		not specified	Uncertain significance (Apr 07, 2022)
1-157521276-C-G			Benign (Jul 16, 2018)
1-157524303-C-T		not specified	Uncertain significance (Nov 30, 2022)
1-157524324-C-A		not specified	Uncertain significance (Dec 01, 2022)
1-157524341-G-C		not specified	Uncertain significance (Feb 05, 2024)
1-157524381-A-C		not specified	Uncertain significance (Jan 03, 2024)
1-157524427-A-G			Benign (Jun 18, 2018)
1-157524453-T-C			Benign (Jul 16, 2018)
1-157524511-C-A		not specified	Uncertain significance (Mar 01, 2023)
1-157527672-C-T			Likely benign (Apr 04, 2018)
1-157527679-G-A		not specified	Uncertain significance (Oct 10, 2023)
1-157527713-G-A		not specified	Uncertain significance (Aug 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FCRL5	protein_coding	protein_coding	ENST00000361835	17	39144

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.61e-17	0.152	125553	0	195	125748	0.000776

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.611	486	525	0.925	0.0000281	6224
Missense in Polyphen		125	157.27	0.79479		2121
Synonymous	-0.0146	216	216	1.00	0.0000117	2068
Loss of Function	1.24	30	38.3	0.784	0.00000163	490

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000327	0.000326
Ashkenazi Jewish	0.00118	0.00109
East Asian	0.000381	0.000381
Finnish	0.00287	0.00287
European (Non-Finnish)	0.000760	0.000756
Middle Eastern	0.000381	0.000381
South Asian	0.000237	0.000229
Other	0.00216	0.00212

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in B-cell development and differentiation in peripheral lymphoid organs and may be useful markers of B-cell stages. May have an immunoregulatory role in marginal zone B-cells. {ECO:0000269|PubMed:11453668}.
• Disease: DISEASE: Note=A chromosomal aberration involving FCRL5 has been found in cell lines with 1q21 abnormalities derived from Burkitt lymphoma. Duplication dup(1)(q21q32). {ECO:0000269|PubMed:11290337}.

Intolerance Scores

• loftool: 0.911
• rvis_EVS: 2.27
• rvis_percentile_EVS: 98.25

Haploinsufficiency Scores

• pHI: 0.0452
• hipred: N
• hipred_score: 0.112
• ghis: 0.418

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.115

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fcrl5

Gene ontology

• Cellular component: plasma membrane;cell surface;integral component of membrane;receptor complex