Brain small vessel disease 3

disease

On this page

Also known as BSVD3

Summary

Brain small vessel disease 3 (MONDO:0100105) is a disease caused by COLGALT1 (GenCC Strong), with 1 cohort gene.

At a glance

Causal gene: COLGALT1 (GenCC Strong)
Cohort genes: 1
ClinVar variants: 10

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	brain small vessel disease 3
Mondo ID	MONDO:0100105
OMIM	618360
DOID	DOID:0112315
UMLS	C5193053
MedGen	1677948
GARD	0026049
Is cancer (heuristic)	no

Also known as: BSVD3

Data availability: 10 ClinVar variants · 4 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by body system or component › nervous system disorder › central nervous system disorder › brain disorder › cerebrovascular disorder › familial porencephaly › brain small vessel disease 3

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

10 retrieved; paginated sample, class counts are floors:

5 uncertain significance, 4 pathogenic, 1 likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
623638	NM_024656.4(COLGALT1):c.452T>G (p.Leu151Arg)	COLGALT1	Pathogenic	no assertion criteria provided
623639	NM_024656.4(COLGALT1):c.1096del (p.Glu366fs)	COLGALT1	Pathogenic	no assertion criteria provided
623640	NM_024656.4(COLGALT1):c.460G>C (p.Ala154Pro)	COLGALT1	Pathogenic	no assertion criteria provided
623641	NM_024656.4(COLGALT1):c.1129G>C (p.Gly377Arg)	COLGALT1	Pathogenic	no assertion criteria provided
917942	NM_024656.4(COLGALT1):c.173T>C (p.Leu58Pro)	COLGALT1	Likely pathogenic	no assertion criteria provided
2039519	NM_024656.4(COLGALT1):c.1147A>G (p.Ser383Gly)	COLGALT1	Uncertain significance	criteria provided, single submitter
2440503	NM_024656.4(COLGALT1):c.1355T>C (p.Met452Thr)	COLGALT1	Uncertain significance	criteria provided, multiple submitters, no conflicts
2440504	NM_024656.4(COLGALT1):c.385G>A (p.Glu129Lys)	COLGALT1	Uncertain significance	criteria provided, multiple submitters, no conflicts
2688853	NM_024656.4(COLGALT1):c.513C>G (p.Ile171Met)	COLGALT1	Uncertain significance	criteria provided, single submitter
3779154	NM_024656.4(COLGALT1):c.1829T>C (p.Leu610Pro)	COLGALT1	Uncertain significance	criteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 4 · Orphanet: 1 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

Gene	Classification	Inheritance	Disease	Records
COLGALT1	Strong	Autosomal recessive	brain small vessel disease 3	4

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
COLGALT1	Orphanet:99810	Familial porencephaly

Cohort genes → proteins

1 cohort genes, 1 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	1

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
COLGALT1	HGNC:26182	ENSG00000130309	Q8NBJ5	Procollagen galactosyltransferase 1	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
COLGALT1	Procollagen galactosyltransferase 1	Beta-galactosyltransferase that transfers beta-galactose to hydroxylysine residues of type I collagen.

Protein-family classification

Druggable: 1 · Difficult: 0 · Unknown: 0 · Druggable fraction: 1.0

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

Family	Genes	Fold	FDR
Enzyme (other)	1	12.0×	0.083

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
COLGALT1	Enzyme (other)	yes	2.4.1.50	Glyco_trans_25, Nucleotide-diphossugar_trans, Collagen_mod_GT25

Expression context

Cohort genes with no expression data: 0.

1 cohort gene are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

Bucket	Genes
narrow (1-5 tissues)	0
moderate (6-20)	0
broad (>20)	1
unknown	0

Top tissues across cohort

Tissue	Cohort genes
granulocyte	1
monocyte	1
stromal cell of endometrium	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
COLGALT1	275	ubiquitous	marker	stromal cell of endometrium, granulocyte, monocyte

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
COLGALT1	930

Structural data

PDB: 1 · AlphaFold-only: 0 · No structure: 0

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
COLGALT1	Q8NBJ5	10

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 1. Enrichment computed across 1 evidence-associated genes (1 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

Pathway	Cohort genes	Fold	FDR	Sample cohort genes
Collagen biosynthesis and modifying enzymes	1	170.4×	0.006	COLGALT1

GO biological processes by enrichment

GO term	Cohort genes	Fold	FDR	Sample cohort genes
positive regulation of collagen fibril organization	1	4213.0×	7e-04	COLGALT1
protein O-linked glycosylation	1	224.7×	0.004	COLGALT1
collagen fibril organization	1	224.7×	0.004	COLGALT1

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 1

Druggability breadth: 1 of 1 evidence-associated genes (100%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
COLGALT1	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

Symbol	Assays	Type breakdown
COLGALT1	1	Binding:1

Cohort enzymes (BRENDA EC)

Symbol	EC numbers	Names
COLGALT1	2.4.1.50	procollagen galactosyltransferase

Pharmacogenomics

Cohort genes with a PharmGKB record: 1; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

0 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	0
B	Phased (≥1) drug, not yet approved	0
C	Druggable family + PDB, no drug	1	COLGALT1
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	0

Undrugged target profiles

1 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

Symbol	ChEMBL assays	Drugged partners (top 3)
COLGALT1	1	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.

Cohort genes: COLGALT1