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AFG2A AFG2 AAA ATPase homolog A [ Homo sapiens (human) ]

Gene ID: 166378, updated on 5-Mar-2024

Summary

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Official Symbol
AFG2Aprovided by HGNC
Official Full Name
AFG2 AAA ATPase homolog Aprovided by HGNC
Primary source
HGNC:HGNC:18119
See related
Ensembl:ENSG00000145375 MIM:613940; AllianceGenome:HGNC:18119
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
AFG2; SPAF; EHLMRS; NEDHSB; SPATA5
Summary
This gene encodes a member of the ATPase associated with diverse activities family, whose members are defined by a highly conserved ATPase domain. Members of this family participate in diverse cellular processes that include membrane fusion, DNA replication, microtubule severing, and protein degradation. The protein encoded by this gene has a putative mitochondrial targeting sequence and has been proposed to function in maintenance of mitochondrial function and integrity during mouse spermatogenesis. Allelic variants in this gene have been associated with epilepsy, hearing loss, and cognitive disability syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]
Expression
Low expression observed in reference dataset See more
Orthologs
mouse all
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Genomic context

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Location:
4q28.1
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (122923078..123319433)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (126227197..126623517)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (123844233..124240588)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900773 Neighboring gene fibroblast growth factor 2 Neighboring gene Sharpr-MPRA regulatory region 4593 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:123843896-123844432 Neighboring gene nudix hydrolase 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:123865949-123866476 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:123866477-123867003 Neighboring gene coilin pseudogene 2 Neighboring gene uncharacterized LOC105377404 Neighboring gene uncharacterized LOC124900772

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Isolated Hearing Impairment Caused by SPATA5 Mutations in a Family with Variable Phenotypic Expression. Szczałuba K, et al. Adv Exp Med Biol, 2017. PMID 28293831
  2. Characterization of SPATA5-related encephalopathy in early childhood. Kurata H, et al. Clin Genet, 2016 Nov. PMID 27246907
  3. Genome-wide pooling approach identifies SPATA5 as a new susceptibility locus for alopecia areata. Forstbauer LM, et al. Eur J Hum Genet, 2012 Mar. PMID 22027810, Free PMC Article
  4. A Genome-wide Association Study for Concussion Risk. Kim SK, et al. Med Sci Sports Exerc, 2021 Apr 1. PMID 33017352
  5. Mutations in SPATA5 Are Associated with Microcephaly, Intellectual Disability, Seizures, and Hearing Loss. Tanaka AJ, et al. Am J Hum Genet, 2015 Sep 3. PMID 26299366, Free PMC Article

See all (81) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Labeling of heterochronic ribosomes reveals C1ORF109 and SPATA5 control a late step in human ribosome assembly.
    Title: Labeling of heterochronic ribosomes reveals C1ORF109 and SPATA5 control a late step in human ribosome assembly.
  2. A Genome-wide Association Study for Concussion Risk.
    Title: A Genome-wide Association Study for Concussion Risk.
  3. Increased DNA methylation in the spermatogenesis-associated (SPATA) genes correlates with infertility.
    Title: Increased DNA methylation in the spermatogenesis-associated (SPATA) genes correlates with infertility.
  4. SPATA5 defects may account for a fraction of isolated sensorineural hearing impairment cases.
    Title: Isolated Hearing Impairment Caused by SPATA5 Mutations in a Family with Variable Phenotypic Expression.
  5. Clinical delineation of the SPATA5-related encephalopathy should improve diagnosis, facilitating further clinical and molecular investigation
    Title: Characterization of SPATA5-related encephalopathy in early childhood.
  6. Mutations in SPATA5 Are Associated with Microcephaly, Intellectual Disability, Seizures, and Hearing Loss.
    Title: Mutations in SPATA5 Are Associated with Microcephaly, Intellectual Disability, Seizures, and Hearing Loss.
  7. SPATA5 locus is a new susceptibility locus for Alopecia areata (AA).
    Title: Genome-wide pooling approach identifies SPATA5 as a new susceptibility locus for alopecia areata.
  8. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study identifies two novel genomic regions in irritable bowel syndrome.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP hydrolysis activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables preribosome binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in brain development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in ribosomal large subunit biogenesis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in spermatogenesis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
  
located_in spindle IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
ATPase family gene 2 protein homolog A
Names
ATPase family gene 2 homolog
ATPase family protein 2 homolog
ribosome biogenesis protein SPATA5
spermatogenesis associated 5
spermatogenesis associated factor SPAF
spermatogenesis-associated factor protein
spermatogenesis-associated protein 5
NP_001304728.1
NP_001332785.1
NP_660208.2
XP_011529980.1
XP_011529981.1
XP_016863314.1
XP_016863316.1
XP_016863318.1
XP_016863319.1
XP_047305646.1
XP_047305647.1
XP_047305648.1
XP_047305649.1
XP_047305650.1
XP_047305651.1
XP_047305652.1
XP_047305653.1
XP_054205046.1
XP_054205047.1
XP_054205048.1
XP_054205049.1
XP_054205050.1
XP_054205051.1
XP_054205052.1
XP_054205053.1
XP_054205054.1
XP_054205055.1
XP_054205056.1
XP_054205057.1
XP_054205058.1
XP_054205059.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_051570.1 RefSeqGene

    Range
    5009..401364
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001317799.2 → NP_001304728.1  ATPase family gene 2 protein homolog A isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, lacks several exons in the 3' coding region and its 3' terminal exon extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC109357, AK091384, BC048217, DA619323
    UniProtKB/Swiss-Prot
    Q8NB90
    Conserved Domains (4) summary
    smart00382
    Location:386 → 524
    AAA; ATPases associated with a variety of cellular activities
    smart01073
    Location:46 → 132
    CDC48_N; Cell division protein 48 (CDC48) N-terminal domain
    pfam00004
    Location:389 → 522
    AAA; ATPase family associated with various cellular activities (AAA)
    cl21455
    Location:663 → 694
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  2. NM_001345856.2 → NP_001332785.1  ATPase family gene 2 protein homolog A isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate, in-frame splice site in the 5' coding region compared to variant 1. It encodes isoform 3, which is shorter than isoform 1.
    Source sequence(s)
    AC021205, AC026402, AC109357

  3. NM_145207.3 → NP_660208.2  ATPase family gene 2 protein homolog A isoform 1

    See identical proteins and their annotated locations for NP_660208.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC026402, AK091384, AL832175, DA619323
    Consensus CDS
    CCDS3730.1
    UniProtKB/Swiss-Prot
    C9JT97, Q86XW1, Q8NB90, Q8NI20, Q8TDL7
    Related
    ENSP00000274008.3, ENST00000274008.5
    Conserved Domains (3) summary
    COG0464
    Location:370 → 882
    SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]
    pfam00004
    Location:664 → 796
    AAA; ATPase family associated with various cellular activities (AAA)
    cl21693
    Location:65 → 133
    CDC48_N; Cell division protein 48 (CDC48), N-terminal domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    122923078..123319433
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017007825.2 → XP_016863314.1  ATPase family gene 2 protein homolog A isoform X1

    Conserved Domains (2) summary
    TIGR01243
    Location:323 → 913
    CDC48; AAA family ATPase, CDC48 subfamily
    cl21693
    Location:65 → 133
    CDC48_N; Cell division protein 48 (CDC48), N-terminal domain

  2. XM_011531678.3 → XP_011529980.1  ATPase family gene 2 protein homolog A isoform X2

    UniProtKB/TrEMBL
    A0A6Q8PGU6
    Related
    ENSP00000502453.1, ENST00000675612.1
    Conserved Domains (2) summary
    smart01073
    Location:46 → 132
    CDC48_N; Cell division protein 48 (CDC48) N-terminal domain
    TIGR01243
    Location:322 → 912
    CDC48; AAA family ATPase, CDC48 subfamily

  3. XM_047449690.1 → XP_047305646.1  ATPase family gene 2 protein homolog A isoform X3

  4. XM_047449691.1 → XP_047305647.1  ATPase family gene 2 protein homolog A isoform X4

  5. XM_047449696.1 → XP_047305652.1  ATPase family gene 2 protein homolog A isoform X10

  6. XM_047449695.1 → XP_047305651.1  ATPase family gene 2 protein homolog A isoform X9

  7. XM_017007827.3 → XP_016863316.1  ATPase family gene 2 protein homolog A isoform X5

    Conserved Domains (2) summary
    TIGR01243
    Location:323 → 803
    CDC48; AAA family ATPase, CDC48 subfamily
    cl21693
    Location:65 → 133
    CDC48_N; Cell division protein 48 (CDC48), N-terminal domain

  8. XM_047449692.1 → XP_047305648.1  ATPase family gene 2 protein homolog A isoform X6

  9. XM_047449693.1 → XP_047305649.1  ATPase family gene 2 protein homolog A isoform X7

  10. XM_011531679.4 → XP_011529981.1  ATPase family gene 2 protein homolog A isoform X11

    UniProtKB/Swiss-Prot
    Q8NB90
    Related
    ENST00000422835.2
    Conserved Domains (2) summary
    TIGR01243
    Location:323 → 779
    CDC48; AAA family ATPase, CDC48 subfamily
    cl21693
    Location:65 → 133
    CDC48_N; Cell division protein 48 (CDC48), N-terminal domain

  11. XM_047449694.1 → XP_047305650.1  ATPase family gene 2 protein homolog A isoform X8

  12. XM_047449697.1 → XP_047305653.1  ATPase family gene 2 protein homolog A isoform X12

  13. XM_017007830.2 → XP_016863319.1  ATPase family gene 2 protein homolog A isoform X14

    Conserved Domains (2) summary
    TIGR01243
    Location:323 → 583
    CDC48; AAA family ATPase, CDC48 subfamily
    cl21693
    Location:65 → 133
    CDC48_N; Cell division protein 48 (CDC48), N-terminal domain

  14. XM_017007829.2 → XP_016863318.1  ATPase family gene 2 protein homolog A isoform X13

    Conserved Domains (1) summary
    TIGR01243
    Location:171 → 761
    CDC48; AAA family ATPase, CDC48 subfamily

RNA

  1. XR_007096375.1 RNA Sequence

  2. XR_007096376.1 RNA Sequence

  3. XR_007096377.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    126227197..126623517
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054349071.1 → XP_054205046.1  ATPase family gene 2 protein homolog A isoform X1

  2. XM_054349072.1 → XP_054205047.1  ATPase family gene 2 protein homolog A isoform X2

    UniProtKB/TrEMBL
    A0A6Q8PGU6

  3. XM_054349073.1 → XP_054205048.1  ATPase family gene 2 protein homolog A isoform X3

  4. XM_054349074.1 → XP_054205049.1  ATPase family gene 2 protein homolog A isoform X4

  5. XM_054349080.1 → XP_054205055.1  ATPase family gene 2 protein homolog A isoform X10

  6. XM_054349075.1 → XP_054205050.1  ATPase family gene 2 protein homolog A isoform X5

  7. XM_054349076.1 → XP_054205051.1  ATPase family gene 2 protein homolog A isoform X6

  8. XM_054349077.1 → XP_054205052.1  ATPase family gene 2 protein homolog A isoform X7

  9. XM_054349081.1 → XP_054205056.1  ATPase family gene 2 protein homolog A isoform X11

  10. XM_054349079.1 → XP_054205054.1  ATPase family gene 2 protein homolog A isoform X9

  11. XM_054349078.1 → XP_054205053.1  ATPase family gene 2 protein homolog A isoform X8

  12. XM_054349082.1 → XP_054205057.1  ATPase family gene 2 protein homolog A isoform X12

  13. XM_054349084.1 → XP_054205059.1  ATPase family gene 2 protein homolog A isoform X14

  14. XM_054349083.1 → XP_054205058.1  ATPase family gene 2 protein homolog A isoform X13

RNA

  1. XR_008486940.1 RNA Sequence

  2. XR_008486941.1 RNA Sequence

  3. XR_008486942.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NB90.3 GenPept UniProtKB/Swiss-Prot:Q8NB90

Gene LinkOut

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