ATAD3B

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

Basic information

Region (hg38): 1:1471765-1497848

Links

ENSG00000160072 ∙ NCBI:83858 ∙ OMIM:612317 ∙ HGNC:24007 ∙ Uniprot:Q5T9A4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATAD3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATAD3B 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				2	1	3
missense			71	9	4	84
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding					1	1
Total	0	0	72	11	6

Variants in ATAD3B

This is a list of pathogenic ClinVar variants found in the ATAD3B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-1471921-G-A		not specified	Uncertain significance (May 24, 2023)
1-1471927-G-A		not specified	Uncertain significance (May 05, 2023)
1-1471931-C-T		not specified	Uncertain significance (Nov 03, 2023)
1-1471937-C-A		not specified	Uncertain significance (Mar 04, 2024)
1-1471946-C-T		not specified	Uncertain significance (Oct 02, 2023)
1-1471966-G-A		not specified	Uncertain significance (Aug 02, 2021)
1-1471988-G-A		not specified	Uncertain significance (Oct 08, 2024)
1-1472044-G-T		not specified	Uncertain significance (Jul 09, 2021)
1-1472059-G-C		not specified	Uncertain significance (Oct 06, 2021)
1-1472063-A-T		not specified	Uncertain significance (Sep 16, 2021)
1-1472081-A-G		not specified	Uncertain significance (Aug 17, 2022)
1-1472082-G-C		not specified	Uncertain significance (Apr 11, 2023)
1-1472084-A-G		not specified	Uncertain significance (Feb 21, 2024)
1-1477279-G-T			Benign (Feb 26, 2018)
1-1477317-G-T		not specified	Uncertain significance (Jun 24, 2022)
1-1477330-G-A		not specified	Uncertain significance (Dec 21, 2023)
1-1477343-A-G			Likely benign (Jun 28, 2017)
1-1478645-A-C		not specified	Uncertain significance (Aug 01, 2024)
1-1478656-G-A		not specified	Uncertain significance (Sep 08, 2024)
1-1478657-C-T		not specified	Uncertain significance (Nov 25, 2024)
1-1478659-G-A		not specified	Uncertain significance (Feb 10, 2022)
1-1478686-C-T		not specified	Uncertain significance (Jan 26, 2022)
1-1478706-G-C		not specified	Uncertain significance (May 28, 2024)
1-1478722-G-A		not specified	Uncertain significance (May 05, 2023)
1-1478725-G-A		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATAD3B	protein_coding	protein_coding	ENST00000308647	16	26086

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00e-22	0.000278	125564	4	160	125728	0.000652

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.79	557	400	1.39	0.0000285	4099
Missense in Polyphen		168	125.08	1.3432		1313
Synonymous	-3.46	233	175	1.33	0.0000128	1328
Loss of Function	-0.497	32	29.1	1.10	0.00000164	336

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00196	0.00195
Ashkenazi Jewish	0.000103	0.0000992
East Asian	0.000819	0.000816
Finnish	0.000187	0.000139
European (Non-Finnish)	0.000683	0.000660
Middle Eastern	0.000819	0.000816
South Asian	0.000333	0.000327
Other	0.000994	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in a mitochondrial network organization typical for stem cells, characterized by reduced mitochondrial metabolism, low mtDNA copies and fragmentated mitochondrial network. may act by suppressing ATAD3A function, interfering with ATAD3A interaction with matrix nucleoid complexes. {ECO:0000269|PubMed:22664726}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.167
• rvis_EVS: 2.17
• rvis_percentile_EVS: 98.03

Haploinsufficiency Scores

• pHI: 0.0853
• hipred: N
• hipred_score: 0.252
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.936

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	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;neutrophil degranulation
• Cellular component: mitochondrion;mitochondrial inner membrane;plasma membrane;secretory granule membrane;ficolin-1-rich granule membrane
• Molecular function: ATP binding;zinc ion binding