ATAD3C

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

Basic information

Region (hg38): 1:1449689-1470163

Links

ENSG00000215915 ∙ NCBI:219293 ∙ OMIM:617227 ∙ HGNC:32151 ∙ Uniprot:Q5T2N8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• pontocerebellar hypoplasia, hypotonia, and respiratory insufficiency syndrome, neonatal lethal (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATAD3C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATAD3C gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			70	6	1	77
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	70	6	1

Variants in ATAD3C

This is a list of pathogenic ClinVar variants found in the ATAD3C region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-1450727-C-T		not specified	Uncertain significance (Oct 16, 2024)
1-1450750-A-G		not specified	Uncertain significance (Dec 28, 2022)
1-1452068-G-A		not specified	Uncertain significance (May 24, 2024)
1-1452074-A-C		not specified	Uncertain significance (Feb 16, 2023)
1-1452104-C-T		not specified	Uncertain significance (Sep 16, 2021)
1-1452119-T-A			Likely benign (Apr 01, 2023)
1-1452409-C-G		not specified	Uncertain significance (Dec 01, 2022)
1-1452433-C-G		not specified	Uncertain significance (Jun 26, 2024)
1-1454394-C-A		not specified	Uncertain significance (Sep 20, 2023)
1-1454394-C-G		not specified	Uncertain significance (Oct 06, 2024)
1-1454394-C-T			Benign (Dec 14, 2018)
1-1454397-C-T		not specified	Uncertain significance (Aug 02, 2022)
1-1454417-A-G		not specified	Uncertain significance (Jun 02, 2023)
1-1454423-G-A		not specified	Uncertain significance (Feb 07, 2023)
1-1454426-C-T		not specified	Uncertain significance (Aug 12, 2021)
1-1454450-A-G		not specified	Uncertain significance (Dec 03, 2024)
1-1454462-C-T		not specified	Uncertain significance (Aug 26, 2024)
1-1454486-C-T		not specified	Uncertain significance (Apr 08, 2024)
1-1455470-G-A		not specified	Uncertain significance (Sep 15, 2021)
1-1455473-G-A		not specified	Uncertain significance (Dec 27, 2023)
1-1455485-G-A		not specified	Uncertain significance (Sep 03, 2024)
1-1455494-A-G		not specified	Uncertain significance (Jul 21, 2021)
1-1455792-C-G		not specified	Uncertain significance (Jun 29, 2023)
1-1455812-C-T		not specified	Conflicting classifications of pathogenicity (Nov 01, 2023)
1-1455821-G-A		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATAD3C	protein_coding	protein_coding	ENST00000378785	12	20470

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.27e-9	0.459	125628	1	102	125731	0.000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.816	302	265	1.14	0.0000182	2611
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000958	0.000876
Ashkenazi Jewish	0.00193	0.00189
East Asian	0.000329	0.000326
Finnish	0.000192	0.000185
European (Non-Finnish)	0.000236	0.000229
Middle Eastern	0.000329	0.000326
South Asian	0.000988	0.000817
Other	0.00100	0.000978

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.441
• rvis_EVS: 2.89
• rvis_percentile_EVS: 99.14

Haploinsufficiency Scores

• pHI: 0.170
• hipred: N
• hipred_score: 0.112
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0729

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atad3a
• Phenotype: muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; skeleton phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: mitochondrion organization
• Cellular component: mitochondrion
• Molecular function: ATP binding;zinc ion binding