FDCSP

protein-coding

follicular dendritic cell secreted protein

Gene summary

This gene encodes a small secreted protein that is expressed in follicular dendritic cells. This protein specifically binds to activated B cells, and functions as a regulator of antibody responses. It is also thought to contribute to tumor metastases by promoting cancer cell migration and invasion. [provided by RefSeq, Dec 2011]

Previous symbols:

C4orf7

MANE transcript

NM_152997.4

Inheritance

—

ClinVar variants

U:16B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr4:70,226,124-70,235,252

External References & Databases

Ensembl (ENSG00000181617)

Transcript & Mutation Effects

hg38 • Region Span ~9.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FDCSP variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 14

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152997.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			15 clinvar	1 clinvar		16
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	16	1	0	17

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152997.4	RefSeq	NP_694542.1	3	MANE Select
ENST00000317987.6	Ensembl	ENSP00000318437.5	3	MANE Select
ENST00001102287.1	Ensembl	ENSP00000772093.1	3	Standard
ENST00001102288.1	Ensembl	ENSP00000772094.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000317987
Coding exons: 3
Length: 9182
Individuals with no LoFs: 124375
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 124380
p: 0.0000201

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0896	48	46.3	1.04	0.00000243	542
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000055	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000092	0.0000089	rare
South Asian	0.000076	0.000067	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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