FSD2

protein-coding

fibronectin type III and SPRY domain containing 2, the group of Fibronectin type III domain containing

Gene summary

This gene encodes a protein that belongs to the FN3/SPRY family of proteins. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

Previous symbols:

SPRYD1

MANE transcript

NM_001007122.4

Inheritance

—

ClinVar variants

U:98B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.95

Max pathogenic AF

—

Genomic locus

chr15:82,755,362-82,806,070

External References & Databases

Ensembl (ENSG00000186628)

Transcript & Mutation Effects

hg38 • Region Span ~50.7 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 FSD2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 99

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001007122.4. 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			98 clinvar	5 clinvar		103
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	98	5	0	103

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001007122.4	RefSeq	NP_001007123.1	12	MANE Select
ENST00000334574.12	Ensembl	ENSP00000335651.8	12	MANE Select
NM_001281805.2	RefSeq	NP_001268734.1	11	Standard
NM_001281806.2	RefSeq	NP_001268735.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

nucleus
sarcoplasmic reticulum
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000334574
Coding exons: 12
Length: 50709
Individuals with no LoFs: 124451
Homozygous LoFs: 0
Heterozygous LoFs: 201
Defined: 124652
p: 0.000807

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.252	377	391	0.964	0.0000201	4925
Missense (PolyPhen)		114	118.52	0.9619		1589
Synonymous	-0.708	161	150	1.07	0.00000871	1380
Loss of Function	0.275	33	34.8	0.950	0.00000183	443

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0023	0.0023	notable
Latino/Admixed American	0.00065	0.00064	rare
Ashkenazi Jewish	0.0025	0.0023	notable
East Asian	0.0020	0.0020	notable
Finnish	0.000093	0.000093	rare
European (Non-Finnish)	0.00048	0.00047	rare
South Asian	0.00098	0.00092	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0927

Intolerance Scores

RVIS EVS: -0.82
RVIS percentile EVS: 11.98

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.149

Gene Damage Prediction

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