FSD1

fibronectin type III and SPRY domain containing 1, the group of Fibronectin type III domain containing

Basic information

Region (hg38): 19:4304598-4323843

Links

ENSG00000105255 ∙ NCBI:79187 ∙ OMIM:609828 ∙ HGNC:13745 ∙ Uniprot:Q9BTV5 ∙ 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 FSD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FSD1 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				4	5	9
missense			41			41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	0	0	41	5	6

Variants in FSD1

This is a list of pathogenic ClinVar variants found in the FSD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-4304760-G-A		not specified	Uncertain significance (Sep 22, 2023)
19-4305985-A-C		not specified	Uncertain significance (Dec 10, 2024)
19-4306030-C-G		not specified	Uncertain significance (Jul 20, 2021)
19-4306253-C-T		not specified	Uncertain significance (Apr 09, 2024)
19-4306316-C-G		not specified	Uncertain significance (Jul 30, 2023)
19-4307887-G-A			Benign (Mar 05, 2018)
19-4307901-C-T		not specified	Uncertain significance (May 30, 2024)
19-4307923-G-A			Benign (Feb 13, 2018)
19-4307992-C-G			Benign (Jul 12, 2018)
19-4310485-G-A		not specified	Uncertain significance (Nov 12, 2024)
19-4310519-T-G		not specified	Uncertain significance (Sep 06, 2022)
19-4310593-C-T		not specified	Uncertain significance (Nov 09, 2022)
19-4311855-C-T		not specified	Likely benign (Dec 27, 2023)
19-4311895-G-A		not specified	Uncertain significance (Jan 29, 2024)
19-4311899-C-A		not specified	Uncertain significance (Dec 16, 2023)
19-4311908-G-T		not specified	Uncertain significance (Oct 06, 2023)
19-4311911-G-A		not specified	Uncertain significance (May 14, 2024)
19-4311918-G-A			Benign (Feb 13, 2018)
19-4311944-A-G		not specified	Uncertain significance (Sep 26, 2022)
19-4311985-C-T		not specified	Uncertain significance (Aug 15, 2024)
19-4312025-T-A		not specified	Uncertain significance (Jan 05, 2022)
19-4312027-C-T		not specified	Uncertain significance (Jun 29, 2022)
19-4312028-G-A		not specified	Uncertain significance (Jan 10, 2023)
19-4312043-C-A		not specified	Uncertain significance (Jan 24, 2025)
19-4317188-A-G		not specified	Uncertain significance (Feb 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FSD1	protein_coding	protein_coding	ENST00000221856	13	19244

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.252	0.748	125737	0	9	125746	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.24	267	330	0.809	0.0000223	3254
Missense in Polyphen		63	84.455	0.74596		809
Synonymous	0.147	133	135	0.984	0.00000952	964
Loss of Function	3.53	6	25.1	0.239	0.00000107	289

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000443	0.0000440
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in microtubule organization and stabilization. {ECO:0000269|PubMed:12154070, ECO:0000269|PubMed:12445389}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.375
• rvis_EVS: -0.89
• rvis_percentile_EVS: 10.43

Haploinsufficiency Scores

• pHI: 0.575
• hipred: Y
• hipred_score: 0.665
• ghis: 0.607

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.728

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fsd1

Gene ontology

• Biological process: cell cycle;cytoplasmic microtubule organization;regulation of cytokinesis;protein homooligomerization;cell division;regulation of cell division;regulation of mitotic spindle organization
• Cellular component: nucleus;cytoplasm;centrosome;microtubule;cleavage furrow
• Molecular function: microtubule binding;protein homodimerization activity