Basal ganglia calcification, idiopathic, 9, autosomal recessive

Summary

Basal ganglia calcification, idiopathic, 9, autosomal recessive (MONDO:0968977) is a disease caused by NAA60 (GenCC Strong), with 1 cohort gene.

At a glance

• Causal gene: NAA60 (GenCC Strong)
• Cohort genes: 1
• ClinVar variants: 6

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	basal ganglia calcification, idiopathic, 9, autosomal recessive
Mondo ID	MONDO:0968977
OMIM	620786
UMLS	C5935607
MedGen	1854926
GARD	0027078
Is cancer (heuristic)	no

Data availability: 6 ClinVar variants · 2 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 › basal ganglia disorder › bilateral striopallidodentate calcinosis › basal ganglia calcification, idiopathic, 9, autosomal recessive

Related subtypes (9): basal ganglia calcification, idiopathic, childhood-onset, 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, 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

6 retrieved; paginated sample, class counts are floors:

6 pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
3076205	NM_001083601.3(NAA60):c.323_329del (p.Arg108fs)	NAA60	Pathogenic	no assertion criteria provided
3076206	NM_001083601.3(NAA60):c.338-1G>C	NAA60	Pathogenic	no assertion criteria provided
3076207	NM_001083601.3(NAA60):c.391C>T (p.His131Tyr)	NAA60	Pathogenic	no assertion criteria provided
3076208	NM_001083601.3(NAA60):c.130C>T (p.Arg44Cys)	NAA60	Pathogenic	no assertion criteria provided
3076209	NM_001083601.3(NAA60):c.50T>G (p.Leu17Arg)	NAA60	Pathogenic	no assertion criteria provided
3076210	NM_001083601.3(NAA60):c.428A>C (p.Asn143Thr)	NAA60	Pathogenic	no assertion criteria provided

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 2 · 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
NAA60	Strong	Autosomal recessive	basal ganglia calcification, idiopathic, 9, autosomal recessive	2

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
NAA60	Orphanet:1980	Bilateral striopallidodentate calcinosis

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
NAA60	HGNC:25875	ENSG00000122390	Q9H7X0	N-alpha-acetyltransferase 60	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
NAA60	N-alpha-acetyltransferase 60	N-alpha-acetyltransferase that specifically mediates the acetylation of N-terminal residues of the transmembrane proteins, with a strong preference for N-termini facing the cytosol.

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)
NAA60	Enzyme (other)	yes	2.3.1.259	GNAT_dom, Acyl_CoA_acyltransferase, NAA60-like

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
endothelial cell	1
ileal mucosa	1
pancreatic ductal cell	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
NAA60	288	ubiquitous	marker	pancreatic ductal cell, endothelial cell, ileal mucosa

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
NAA60	974

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
NAA60	Q9H7X0	5

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 0. Enrichment computed across 1 evidence-associated genes (0 with Reactome annotation).

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
N-terminal peptidyl-methionine acetylation	1	16852.0×	3e-04	NAA60
N-terminal protein amino acid acetylation	1	3370.4×	7e-04	NAA60
chromosome segregation	1	173.7×	0.009	NAA60
nucleosome assembly	1	140.4×	0.009	NAA60
cell population proliferation	1	102.8×	0.010	NAA60

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
NAA60	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
NAA60	1	Binding:1

Cohort enzymes (BRENDA EC)

Symbol	EC numbers	Names
NAA60	2.3.1.259	N-terminal methionine Nalpha-acetyltransferase NatF

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	NAA60
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)
NAA60	1	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.