FCRL1

Fc receptor like 1, the group of CD molecules|Immunoglobulin like domain containing|Fc receptors

Basic information

Region (hg38): 1:157792249-157820120

Links

ENSG00000163534 ∙ NCBI:115350 ∙ OMIM:606508 ∙ HGNC:18509 ∙ Uniprot:Q96LA6 ∙ 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 FCRL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FCRL1 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	0

Variants in FCRL1

This is a list of pathogenic ClinVar variants found in the FCRL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-157796128-T-C		not specified	Uncertain significance (May 23, 2023)
1-157796165-G-A		not specified	Likely benign (Nov 29, 2023)
1-157797118-T-A		not specified	Uncertain significance (Dec 18, 2023)
1-157797921-T-C		not specified	Uncertain significance (Jan 23, 2023)
1-157798196-G-A		not specified	Uncertain significance (Mar 20, 2023)
1-157798206-G-T		not specified	Uncertain significance (Jul 12, 2022)
1-157800085-C-T		not specified	Uncertain significance (Sep 16, 2021)
1-157801921-A-G		not specified	Uncertain significance (Dec 06, 2022)
1-157802037-G-T		not specified	Uncertain significance (Dec 15, 2023)
1-157802048-G-C		not specified	Uncertain significance (Dec 27, 2023)
1-157802131-C-T		not specified	Uncertain significance (Apr 15, 2024)
1-157802133-T-C		not specified	Uncertain significance (Mar 19, 2024)
1-157802505-G-A		not specified	Uncertain significance (Jun 30, 2022)
1-157802650-C-T		not specified	Likely benign (Jan 10, 2023)
1-157802664-C-G		not specified	Uncertain significance (Jun 05, 2023)
1-157803899-G-C		not specified	Uncertain significance (Mar 19, 2024)
1-157803916-G-A		not specified	Uncertain significance (Sep 29, 2022)
1-157803955-T-C		not specified	Uncertain significance (Aug 16, 2022)
1-157803993-G-T		not specified	Uncertain significance (Mar 01, 2024)
1-157804054-G-A		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FCRL1	protein_coding	protein_coding	ENST00000368176	11	25703

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000395	0.954	125628	0	111	125739	0.000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0643	234	237	0.988	0.0000123	2755
Missense in Polyphen		47	59.224	0.79359		794
Synonymous	-1.17	110	95.5	1.15	0.00000521	867
Loss of Function	1.87	12	21.3	0.563	9.06e-7	264

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000218
Finnish	0.00102	0.00102
European (Non-Finnish)	0.000656	0.000651
Middle Eastern	0.000218	0.000218
South Asian	0.0000653	0.0000653
Other	0.000985	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as an activating coreceptor in B-cells. May function in B-cells activation and differentiation. {ECO:0000269|PubMed:15479727}.

Recessive Scores

• pRec: 0.0890

Intolerance Scores

• loftool: 0.740
• rvis_EVS: 0.64
• rvis_percentile_EVS: 84.1

Haploinsufficiency Scores

• pHI: 0.0790
• hipred: N
• hipred_score: 0.158
• ghis: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0785

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fcrl1

Gene ontology

• Biological process: B cell activation
• Cellular component: plasma membrane;cell surface;integral component of membrane
• Molecular function: coreceptor activity