FDCSP

follicular dendritic cell secreted protein

Basic information

Region (hg38): 4:70226123-70235252

Previous symbols: [ "C4orf7" ]

Links

ENSG00000181617 ∙ NCBI:260436 ∙ OMIM:607241 ∙ HGNC:19215 ∙ Uniprot:Q8NFU4 ∙ 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 FDCSP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FDCSP 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in FDCSP

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

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

Position	Type	Phenotype	Significance	ClinVar
4-70233013-G-A		not specified	Uncertain significance (Apr 27, 2022)
4-70234032-G-A		not specified	Likely benign (Feb 09, 2023)
4-70234065-T-C		not specified	Uncertain significance (Jan 29, 2024)
4-70234066-A-C		not specified	Uncertain significance (Mar 24, 2023)
4-70234080-C-T		not specified	Uncertain significance (Feb 13, 2024)
4-70234083-C-T		not specified	Uncertain significance (Oct 25, 2022)
4-70234124-A-C		not specified	Uncertain significance (Nov 08, 2022)
4-70234167-C-T		not specified	Uncertain significance (Feb 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FDCSP	protein_coding	protein_coding	ENST00000317987	3	9182

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0818	0.768	124375	0	5	124380	0.0000201

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0896	48	46.3	1.04	0.00000243	542
Missense in Polyphen		2	2.0835	0.95993		26
Synonymous	0.115	15	15.6	0.963	8.28e-7	166
Loss of Function	1.05	2	4.38	0.457	2.80e-7	47

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000648	0.0000622
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000552	0.0000546
Finnish	0.00	0.00
European (Non-Finnish)	0.00000922	0.00000886
Middle Eastern	0.0000552	0.0000546
South Asian	0.0000765	0.0000667
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Can bind to the surface of B-lymphoma cells, but not T- lymphoma cells, consistent with a function as a secreted mediator acting upon B-cells.

Recessive Scores

• pRec: 0.0319

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• pHI: 0.0102
• hipred: N
• hipred_score: 0.123
• ghis: 0.432

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Cellular component: extracellular region