ATAD3C

protein-coding

ATPase family AAA domain containing 3C, the group of AAA ATPases

Gene summary

Predicted to enable ATP binding activity and ATP hydrolysis activity. Predicted to be involved in mitochondrion organization. Predicted to be active in mitochondrion. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001039211.3

Inheritance

—

ClinVar variants

U:120B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr1:1,449,689-1,470,163

External References & Databases

Ensembl (ENSG00000215915)

Transcript & Mutation Effects

hg38 • Region Span ~20.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

pontocerebellar hypoplasia, hypotonia, and respiratory insufficiency syndrome, neonatal lethalLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0032931

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATAD3C variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 122

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001039211.3. 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			2 clinvar	1 clinvar		3
missense			117 clinvar	10 clinvar	1 clinvar	128
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	120	11	1	132

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001039211.3	RefSeq	NP_001034300.2	12	MANE Select
ENST00000378785.7	Ensembl	ENSP00000368062.2	12	MANE Select
ENST00000475091.2	Ensembl	ENSP00000464661.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mitochondrion organization

Molecular Function

ATP binding
zinc ion binding

Cellular Component

mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000378785
Coding exons: 12
Length: 20470
Individuals with no LoFs: 125628
Homozygous LoFs: 1
Heterozygous LoFs: 102
Defined: 125731
p: 0.000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.816	302	265	1.14	0.0000182	2611
Missense (PolyPhen)		73	63.634	1.1472		594
Synonymous	-1.40	135	116	1.17	0.00000839	823
Loss of Function	0.976	15	19.7	0.763	9.84e-7	225

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00070	0.00062	rare
Latino/Admixed American	0.00026	0.00020	rare
Ashkenazi Jewish	0.0019	0.0019	notable
East Asian	0.00033	0.00033	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00024	0.00023	rare
South Asian	0.00099	0.00082	rare
Other	0.0010	0.00098	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.441
RVIS EVS: 2.89
RVIS percentile EVS: 99.14

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0729

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	High	Medium	High