Basal ganglia calcification, idiopathic, childhood-onset

Summary

Basal ganglia calcification, idiopathic, childhood-onset (MONDO:0007247) is a disease with 1 cohort gene.

At a glance

• Cohort genes: 1
• ClinVar variants: 3

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	basal ganglia calcification, idiopathic, childhood-onset
Mondo ID	MONDO:0007247
MeSH	C536276
OMIM	114100
UMLS	C1861967
MedGen	396262
GARD	0009598
Is cancer (heuristic)	no

Also known as: basal ganglia calcification, idiopathic, childhood-onset · bilateral striopallidodentate calcinosis childhood-onset · cerebral calcification nonarteriosclerotic idiopathic childhood-onset · IBGC childhood onset · idiopathic basal ganglia calcification childhood-onset

Data availability: 3 ClinVar variants.

Disease family

Classification path: disease › human disease › disease by body system or component › nervous system disorder › central nervous system disorder › brain disorder › basal ganglia disorder › bilateral striopallidodentate calcinosis › basal ganglia calcification, idiopathic, childhood-onset

Related subtypes (9): basal ganglia calcification, idiopathic, 4, basal ganglia calcification, idiopathic, 5, basal ganglia calcification, idiopathic, 6, basal ganglia calcification, idiopathic, 1, basal ganglia calcification, idiopathic, 7, autosomal recessive, basal ganglia calcification, idiopathic, 8, autosomal recessive, basal ganglia calcification, idiopathic, 9, autosomal recessive, basal ganglia calcification, idiopathic, 10, autosomal recessive, basal ganglia calcification, idiopathic, 11, autosomal recessive

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

3 retrieved; paginated sample, class counts are floors:

2 conflicting classifications of pathogenicity, 1 uncertain significance

ClinVar	Variant (HGVS)	Gene	Classification	Review
703989	NM_022168.4(IFIH1):c.229C>T (p.Arg77Trp)	IFIH1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
849039	NM_022168.4(IFIH1):c.1853G>A (p.Arg618Gln)	IFIH1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
2672248	NM_022168.4(IFIH1):c.2947A>G (p.Lys983Glu)	IFIH1	Uncertain significance	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 3 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
IFIH1	Orphanet:51	Aicardi-Goutières syndrome
IFIH1	Orphanet:689231	IFIH1-related hereditary spastic paraplegia
IFIH1	Orphanet:85191	Singleton-Merten dysplasia

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
IFIH1	HGNC:18873	ENSG00000115267	Q9BYX4	Interferon-induced helicase C domain-containing protein 1	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
IFIH1	Interferon-induced helicase C domain-containing protein 1	Innate immune receptor which acts as a cytoplasmic sensor of viral nucleic acids and plays a major role in sensing viral infection and in the activation of a cascade of antiviral responses including the induction of type I interferons and…

Protein-family classification

Druggable: 0 · Difficult: 0 · Unknown: 1 · Druggable fraction: 0.0

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
Other/Unknown	1	1.8×	0.558

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
IFIH1	Other/Unknown	no		Helicase_C-like, Helicase/UvrB_N, DEATH-like_dom_sf

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
jejunal mucosa	1
palpebral conjunctiva	1
parotid gland	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
IFIH1	276	ubiquitous	marker	palpebral conjunctiva, parotid gland, jejunal mucosa

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
IFIH1	3,706

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
IFIH1	Q9BYX4	9

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 13. 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
NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10	1	878.5×	0.005	IFIH1
TRAF3-dependent IRF activation pathway	1	761.3×	0.005	IFIH1
Modulation of host responses by IFN-stimulated genes	1	601.0×	0.005	IFIH1
TRAF6 mediated NF-kB activation	1	456.8×	0.005	IFIH1
TRAF6 mediated IRF7 activation	1	380.7×	0.005	IFIH1
Dengue virus activates/modulates innate and adaptive immune responses	1	335.9×	0.005	IFIH1
Negative regulators of DDX58/IFIH1 signaling	1	326.3×	0.005	IFIH1
Evasion by RSV of host interferon responses	1	326.3×	0.005	IFIH1
Ovarian tumor domain proteases	1	278.5×	0.005	IFIH1
SARS-CoV-1 activates/modulates innate immune responses	1	271.9×	0.005	IFIH1
DDX58/IFIH1-mediated induction of interferon-alpha/beta	1	253.8×	0.005	IFIH1
SARS-CoV-2 activates/modulates innate and adaptive immune responses	1	89.2×	0.012	IFIH1
Ub-specific processing proteases	1	53.1×	0.019	IFIH1

GO biological processes 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.

GO term	Cohort genes	Fold	FDR	Sample cohort genes
regulation of type III interferon production	1	8426.0×	0.002	IFIH1
detection of virus	1	4213.0×	0.002	IFIH1
MDA-5 signaling pathway	1	4213.0×	0.002	IFIH1
positive regulation of response to cytokine stimulus	1	2407.4×	0.002	IFIH1
cellular response to exogenous dsRNA	1	1053.2×	0.004	IFIH1
cytoplasmic pattern recognition receptor signaling pathway	1	887.0×	0.004	IFIH1
protein complex oligomerization	1	674.1×	0.004	IFIH1
positive regulation of interferon-alpha production	1	648.1×	0.004	IFIH1
positive regulation of interferon-beta production	1	391.9×	0.005	IFIH1
negative regulation of viral genome replication	1	374.5×	0.005	IFIH1
type I interferon-mediated signaling pathway	1	343.9×	0.005	IFIH1
protein sumoylation	1	324.1×	0.005	IFIH1
antiviral innate immune response	1	227.7×	0.006	IFIH1
cellular response to virus	1	200.6×	0.007	IFIH1
positive regulation of interleukin-6 production	1	166.8×	0.008	IFIH1
positive regulation of tumor necrosis factor production	1	153.2×	0.008	IFIH1
response to virus	1	144.0×	0.008	IFIH1
defense response to virus	1	69.3×	0.015	IFIH1
innate immune response	1	33.6×	0.030	IFIH1

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
IFIH1	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

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

Symbol	Assays	Type breakdown
IFIH1	1	Binding:1

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	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	1	IFIH1

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)
IFIH1	1	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.