FCRL2

Fc receptor like 2, the group of CD molecules|Fc receptors|Immunoglobulin like domain containing

Basic information

Region (hg38): 1:157745733-157777132

Previous symbols: [ "SPAP1" ]

Links

ENSG00000132704 ∙ NCBI:79368 ∙ OMIM:606509 ∙ HGNC:14875 ∙ Uniprot:Q96LA5 ∙ 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 FCRL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FCRL2 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						0
missense			36	3		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	3	0

Variants in FCRL2

This is a list of pathogenic ClinVar variants found in the FCRL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-157746749-A-T		not specified	Uncertain significance (Feb 25, 2025)
1-157746774-C-T		not specified	Uncertain significance (Mar 06, 2023)
1-157746873-T-G		not specified	Uncertain significance (Feb 26, 2025)
1-157748606-T-A		not specified	Uncertain significance (Feb 05, 2024)
1-157748925-T-C		not specified	Uncertain significance (Jun 29, 2023)
1-157748956-C-G		not specified	Uncertain significance (Nov 21, 2023)
1-157749654-G-C		not specified	Uncertain significance (Aug 02, 2023)
1-157766902-A-T		not specified	Uncertain significance (Sep 22, 2023)
1-157767239-G-A		not specified	Uncertain significance (May 26, 2024)
1-157767276-C-T		not specified	Uncertain significance (May 05, 2022)
1-157767281-T-C		not specified	Uncertain significance (Aug 02, 2023)
1-157767374-G-C		not specified	Uncertain significance (Nov 27, 2023)
1-157767378-C-T		not specified	Likely benign (Feb 03, 2022)
1-157767405-T-C		not specified	Uncertain significance (Nov 27, 2023)
1-157767407-G-T		not specified	Uncertain significance (Aug 14, 2024)
1-157767428-T-C		not specified	Uncertain significance (Aug 04, 2023)
1-157767497-C-T		not specified	Uncertain significance (Oct 05, 2023)
1-157767498-G-A		not specified	Uncertain significance (Oct 20, 2023)
1-157768419-A-C		not specified	Uncertain significance (Jun 06, 2023)
1-157768447-T-C		not specified	Uncertain significance (Jul 27, 2022)
1-157768450-G-A		not specified	Likely benign (Mar 10, 2025)
1-157768455-T-C		not specified	Uncertain significance (Jun 09, 2022)
1-157768486-C-T		not specified	Uncertain significance (Aug 08, 2023)
1-157768580-C-A		not specified	Uncertain significance (Apr 09, 2024)
1-157768590-G-A		not specified	Uncertain significance (Apr 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FCRL2	protein_coding	protein_coding	ENST00000361516	12	31400

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.45e-11	0.339	125722	0	24	125746	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.480	290	268	1.08	0.0000133	3287
Missense in Polyphen		61	63.904	0.95456		790
Synonymous	-0.869	119	108	1.11	0.00000577	1013
Loss of Function	1.08	20	25.9	0.772	0.00000110	312

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have an regulatory role in normal and neoplastic B cell development. {ECO:0000269|PubMed:11493702}.

Recessive Scores

• pRec: 0.0777

Intolerance Scores

• loftool: 0.655
• rvis_EVS: -0.2
• rvis_percentile_EVS: 39.17

Haploinsufficiency Scores

• pHI: 0.154
• hipred: N
• hipred_score: 0.158
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0330

Gene Damage Prediction

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

Gene ontology

• Biological process: cell-cell signaling;positive regulation of signal transduction
• Cellular component: plasma membrane;cell surface;integral component of membrane
• Molecular function: SH3/SH2 adaptor activity;protein binding