FSD2

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

Basic information

Region (hg38): 15:82755362-82806070

Previous symbols: [ "SPRYD1" ]

Links

ENSG00000186628 ∙ NCBI:123722 ∙ ∙ HGNC:18024 ∙ Uniprot:A1L4K1 ∙ 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 FSD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FSD2 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			56	3		59
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	3	0

Variants in FSD2

This is a list of pathogenic ClinVar variants found in the FSD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-82759374-T-C		not specified	Uncertain significance (Apr 20, 2023)
15-82759425-A-G		not specified	Uncertain significance (Jan 23, 2025)
15-82759466-A-G		not specified	Uncertain significance (Jun 11, 2024)
15-82759503-T-C		not specified	Uncertain significance (Mar 04, 2025)
15-82759530-C-T		not specified	Uncertain significance (Feb 06, 2023)
15-82759532-A-G		not specified	Uncertain significance (Oct 03, 2024)
15-82759542-G-T		not specified	Uncertain significance (Dec 15, 2023)
15-82759587-A-G		not specified	Uncertain significance (Jun 23, 2023)
15-82759594-C-G		not specified	Uncertain significance (Feb 13, 2025)
15-82759598-T-C		not specified	Uncertain significance (Jul 22, 2022)
15-82762174-T-C		not specified	Uncertain significance (Aug 14, 2024)
15-82762190-C-G		not specified	Uncertain significance (Mar 22, 2023)
15-82762273-A-C		not specified	Uncertain significance (Jan 08, 2024)
15-82765182-C-A		not specified	Uncertain significance (Mar 25, 2024)
15-82765182-C-G		not specified	Uncertain significance (Nov 10, 2024)
15-82765182-C-T		not specified	Uncertain significance (Feb 07, 2025)
15-82765223-C-T		not specified	Uncertain significance (Jun 27, 2023)
15-82765232-G-A		not specified	Uncertain significance (Mar 06, 2023)
15-82765271-G-A		not specified	Uncertain significance (Feb 07, 2025)
15-82765286-C-T		not specified	Likely benign (Mar 04, 2024)
15-82765288-A-C		not specified	Uncertain significance (Nov 08, 2024)
15-82765900-A-G		not specified	Likely benign (Jul 06, 2021)
15-82765927-C-T		not specified	Uncertain significance (Oct 30, 2023)
15-82765931-C-T		not specified	Uncertain significance (Dec 15, 2023)
15-82765936-G-A		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FSD2	protein_coding	protein_coding	ENST00000334574	12	50709

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.53e-21	0.00266	124451	0	201	124652	0.000807

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.252	377	391	0.964	0.0000201	4925
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00294	0.00291
Ashkenazi Jewish	0.00249	0.00229
East Asian	0.00203	0.00200
Finnish	0.0000929	0.0000928
European (Non-Finnish)	0.000475	0.000469
Middle Eastern	0.00203	0.00200
South Asian	0.000975	0.000915
Other	0.000332	0.000330

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0927

Intolerance Scores

• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.98

Haploinsufficiency Scores

• pHI: 0.0650
• hipred: N
• hipred_score: 0.167
• ghis: 0.517

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.149

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fsd2

Gene ontology

• Cellular component: nucleus;sarcoplasmic reticulum;perinuclear region of cytoplasm
• Molecular function: protein binding