BORCS5

protein-coding

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

Gene summary

Involved in lysosome localization and organelle transport along microtubule. Located in cytoplasmic side of lysosomal membrane and plus-end kinesin complex. Part of BORC complex. Implicated in colorectal adenocarcinoma. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

LOH12CR1

MANE transcript

NM_058169.6

Inheritance

ClinVar variants

P:9U:27B:1

Top phenotype

NEURODEGENERATION, INFANTILE-ONSET, WITH OPTIC ATROPHY AND STRUCTURAL BRAIN ABNORMALITIES 2

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr12:12,357,078-12,471,233

External References & Databases

Ensembl (ENSG00000165714)

Transcript & Mutation Effects

hg38 • Region Span ~114.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

complex neurodevelopmental disorderLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0100038

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BORCS5 variants in ClinVar

10 Conditions Cataloged

not specifiedTotal: 27

NEURODEGENERATION, INFANTILE-ONSET, WITH OPTIC ATROPHY AND STRUCTURAL BRAIN ABNORMALITIES 2Total: 7

not providedTotal: 1

BORCS5-related disorderTotal: 1

PolymicrogyriaTotal: 1

Corpus callosum, agenesis ofTotal: 1

SeizureTotal: 1

Global developmental delayTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_058169.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense	2 clinvar		27 clinvar	1 clinvar		30
nonsense	2 clinvar					2
start loss						0
frameshift	2 clinvar	1 clinvar				3
splice donor/acceptor (+/-2bp)	1 clinvar	1 clinvar				2
Total	7	2	27	1	0	37

Highest pathogenic variant AF is 0.000015491061

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_058169.6	RefSeq	NP_477517.1	4	MANE Select
ENST00000314565.9	Ensembl	ENSP00000321546.4	4	MANE Select
NM_001300742.3	RefSeq	NP_001287671.1	4	Standard
NM_001330356.2	RefSeq	NP_001317285.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

lysosome localization
organelle transport along microtubule

Molecular Function

protein binding

Cellular Component

plus-end kinesin complex
intrinsic component of membrane
cytoplasmic side of lysosomal membrane
BORC complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000314565
Coding exons: 4
Length: 109828
Individuals with no LoFs: 125734
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125748
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.259	113	121	0.934	0.00000727	1289
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.00016	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (gene trap): N