BSDC1

BSD domain containing 1

Basic information

Region (hg38): 1:32364632-32394731

Links

ENSG00000160058 ∙ NCBI:55108 ∙ OMIM:617518 ∙ HGNC:25501 ∙ Uniprot:Q9NW68 ∙ 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 BSDC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BSDC1 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			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	0

Variants in BSDC1

This is a list of pathogenic ClinVar variants found in the BSDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-32368452-C-T		not specified	Uncertain significance (Jan 03, 2024)
1-32368454-G-A		not specified	Uncertain significance (Apr 07, 2022)
1-32368478-A-G		not specified	Uncertain significance (Mar 01, 2023)
1-32368536-T-C		not specified	Uncertain significance (Mar 12, 2024)
1-32376274-T-C		not specified	Uncertain significance (Sep 17, 2021)
1-32376447-C-T		not specified	Uncertain significance (Feb 22, 2023)
1-32376579-C-T		not specified	Uncertain significance (Feb 22, 2023)
1-32376598-C-A		not specified	Uncertain significance (Sep 17, 2021)
1-32376611-C-A		not specified	Uncertain significance (Aug 02, 2021)
1-32376697-C-T		not specified	Uncertain significance (Sep 07, 2022)
1-32376729-C-A		not specified	Uncertain significance (Aug 10, 2021)
1-32378005-C-T		not specified	Uncertain significance (Sep 27, 2021)
1-32378045-G-C		not specified	Uncertain significance (Sep 29, 2023)
1-32378227-A-T		not specified	Uncertain significance (Nov 15, 2021)
1-32378793-C-G		not specified	Uncertain significance (Jul 09, 2021)
1-32378800-C-A		not specified	Uncertain significance (Nov 07, 2022)
1-32381228-C-T		not specified	Uncertain significance (Mar 07, 2023)
1-32381258-T-C		not specified	Uncertain significance (Sep 14, 2021)
1-32381264-C-T		not specified	Uncertain significance (Apr 09, 2024)
1-32383898-T-A		not specified	Uncertain significance (May 24, 2023)
1-32383979-C-T		not specified	Uncertain significance (Apr 26, 2024)
1-32383990-C-T		not specified	Uncertain significance (Oct 10, 2023)
1-32386867-C-T		not specified	Uncertain significance (Mar 16, 2024)
1-32386880-C-T		not specified	Uncertain significance (Dec 21, 2023)
1-32386886-C-T		not specified	Uncertain significance (Oct 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BSDC1	protein_coding	protein_coding	ENST00000446293	11	29629

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0241	0.975	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.628	219	247	0.888	0.0000141	2878
Missense in Polyphen		50	72.643	0.6883		894
Synonymous	0.575	97	104	0.928	0.00000678	882
Loss of Function	3.03	7	22.5	0.311	0.00000104	288

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000706	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0905

Intolerance Scores

• loftool: 0.0968
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.25

Haploinsufficiency Scores

• pHI: 0.633
• hipred: Y
• hipred_score: 0.581
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.621

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bsdc1