BSPRY

B-box and SPRY domain containing

Basic information

Region (hg38): 9:113349541-113371233

Links

ENSG00000119411 ∙ NCBI:54836 ∙ OMIM:619683 ∙ HGNC:18232 ∙ Uniprot:Q5W0U4 ∙ 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 BSPRY gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BSPRY 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				1		1
missense			39			39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	1	0

Variants in BSPRY

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

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

Position	Type	Phenotype	Significance	ClinVar
9-113349608-C-T		not specified	Uncertain significance (Dec 11, 2023)
9-113349632-C-T		not specified	Uncertain significance (Apr 15, 2024)
9-113349640-C-T		not specified	Uncertain significance (Jul 20, 2021)
9-113349651-A-C		not specified	Uncertain significance (Dec 19, 2023)
9-113349665-T-G		not specified	Uncertain significance (Nov 08, 2022)
9-113349724-G-C		not specified	Uncertain significance (May 05, 2023)
9-113349733-C-T		not specified	Uncertain significance (Apr 06, 2022)
9-113349748-C-T		not specified	Uncertain significance (Oct 30, 2023)
9-113349752-G-T		not specified	Uncertain significance (Aug 14, 2023)
9-113354243-A-G		not specified	Uncertain significance (Aug 22, 2023)
9-113354316-C-T		not specified	Uncertain significance (Dec 06, 2023)
9-113354319-G-C		not specified	Uncertain significance (Jul 26, 2022)
9-113360508-G-A		not specified	Uncertain significance (Sep 12, 2023)
9-113360563-T-G		not specified	Uncertain significance (Sep 14, 2022)
9-113360585-C-T		not specified	Uncertain significance (Feb 13, 2024)
9-113360625-A-C		not specified	Uncertain significance (Jan 29, 2024)
9-113360640-C-T		not specified	Uncertain significance (Jan 19, 2024)
9-113360687-C-T		not specified	Uncertain significance (Dec 02, 2022)
9-113368272-G-A		not specified	Uncertain significance (Dec 07, 2021)
9-113368313-T-C		not specified	Likely benign (Oct 25, 2023)
9-113368360-C-T		not specified	Uncertain significance (Aug 12, 2021)
9-113369630-C-T		not specified	Uncertain significance (Nov 10, 2021)
9-113369631-G-A		not specified	Uncertain significance (Nov 29, 2023)
9-113369636-G-A		not specified	Uncertain significance (May 18, 2023)
9-113369643-G-A		not specified	Uncertain significance (Jan 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BSPRY	protein_coding	protein_coding	ENST00000374183	6	21693

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000133	0.621	124821	0	38	124859	0.000152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.129	209	214	0.975	0.0000133	2568
Missense in Polyphen		63	70.09	0.89885		862
Synonymous	0.565	85	91.9	0.925	0.00000594	830
Loss of Function	0.990	11	15.2	0.726	7.13e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000695	0.000672
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.0000556	0.0000556
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000164	0.000159
Middle Eastern	0.0000556	0.0000556
South Asian	0.000132	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate epithelial calcium transport by inhibiting TRPV5 activity. {ECO:0000250}.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.697
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.38

Haploinsufficiency Scores

• pHI: 0.545
• hipred: N
• hipred_score: 0.197
• ghis: 0.469

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.227

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bspry

Gene ontology

• Biological process: calcium ion transport;cellular response to leukemia inhibitory factor
• Cellular component: membrane;cell leading edge;perinuclear region of cytoplasm
• Molecular function: zinc ion binding