BORCS5

BLOC-1 related complex subunit 5, the group of BLOC-1 related complex subunits

Basic information

Region (hg38): 12:12357078-12471233

Previous symbols: [ "LOH12CR1" ]

Links

ENSG00000165714 ∙ NCBI:118426 ∙ OMIM:616598 ∙ HGNC:17950 ∙ Uniprot:Q969J3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BORCS5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BORCS5 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in BORCS5

This is a list of pathogenic ClinVar variants found in the BORCS5 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-12361211-C-A		not specified	Uncertain significance (Oct 06, 2022)
12-12361223-A-G		not specified	Uncertain significance (Nov 18, 2022)
12-12361281-G-A		not specified	Uncertain significance (Feb 16, 2023)
12-12361286-G-A		not specified	Uncertain significance (Nov 21, 2022)
12-12435627-G-T		6 conditions	Conflicting classifications of pathogenicity (Oct 17, 2024)
12-12435661-C-A		not specified	Uncertain significance (Aug 02, 2021)
12-12435779-C-G		not specified	Uncertain significance (Jan 08, 2024)
12-12465645-G-A		not specified	Uncertain significance (Jan 04, 2024)
12-12465687-C-T		not specified	Uncertain significance (Jun 13, 2022)
12-12465718-C-A		not specified	Uncertain significance (Dec 13, 2023)
12-12465753-C-A		not specified	Uncertain significance (Feb 27, 2024)
12-12465757-A-G		not specified	Uncertain significance (Aug 08, 2023)
12-12465759-C-T		not specified	Uncertain significance (Jun 11, 2021)
12-12465760-G-A		not specified	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BORCS5	protein_coding	protein_coding	ENST00000314565	4	109828

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00124	0.863	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.259	113	121	0.934	0.00000727	1289
Missense in Polyphen		28	34.739	0.80601		374
Synonymous	-1.16	61	50.5	1.21	0.00000336	377
Loss of Function	1.29	6	10.5	0.571	6.34e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As part of the BORC complex may play a role in lysosomes movement and localization at the cell periphery. Associated with the cytosolic face of lysosomes, the BORC complex may recruit ARL8B and couple lysosomes to microtubule plus-end-directed kinesin motor. Thereby, it may indirectly play a role in cell spreading and motility. {ECO:0000269|PubMed:25898167}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

• pHI: 0.192
• hipred: N
• hipred_score: 0.444
• ghis: 0.408

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Borcs5

Gene ontology

• Biological process: lysosome localization;organelle transport along microtubule
• Cellular component: plus-end kinesin complex;intrinsic component of membrane;cytoplasmic side of lysosomal membrane;BORC complex
• Molecular function: protein binding