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AFG2B AFG2 AAA ATPase homolog B [ Homo sapiens (human) ]

Gene ID: 79029, updated on 3-Nov-2024

Summary

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Official Symbol
AFG2Bprovided by HGNC
Official Full Name
AFG2 AAA ATPase homolog Bprovided by HGNC
Primary source
HGNC:HGNC:28762
See related
Ensembl:ENSG00000171763 MIM:619578; AllianceGenome:HGNC:28762
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NEDHLS; DFNB119; SPATA5L1
Summary
Enables preribosome binding activity. Involved in ribosomal large subunit biogenesis. Located in cytoplasm and spindle. Implicated in autosomal recessive nonsyndromic deafness. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in esophagus (RPKM 2.7), bone marrow (RPKM 1.8) and 25 other tissues See more
Orthologs
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Genomic context

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See AFG2B in Genome Data Viewer
Location:
15q21.1
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (45402336..45421415)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (43210511..43229587)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (45694534..45713613)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 953, pseudogene Neighboring gene glycine amidinotransferase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9359 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9360 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6407 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:45716799-45717298 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6409 Neighboring gene uncharacterized LOC107987223 Neighboring gene chromosome 15 open reading frame 48 Neighboring gene microRNA 147b

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 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. Bi-allelic variants in SPATA5L1 lead to intellectual disability, spastic-dystonic cerebral palsy, epilepsy, and hearing loss. Richard EM, et al. Am J Hum Genet, 2021 Oct 7. PMID 34626583, Free PMC Article
  2. Labeling of heterochronic ribosomes reveals C1ORF109 and SPATA5 control a late step in human ribosome assembly. Ni C, et al. Cell Rep, 2022 Mar 29. PMID 35354024, Free PMC Article
  3. Using multiple measures for quantitative trait association analyses: application to estimated glomerular filtration rate. Tin A, et al. J Hum Genet, 2013 Jul. PMID 23535967, Free PMC Article
  4. Multiple loci associated with indices of renal function and chronic kidney disease. Köttgen A, et al. Nat Genet, 2009 Jun. PMID 19430482, Free PMC Article
  5. EML3 is a nuclear microtubule-binding protein required for the correct alignment of chromosomes in metaphase. Tegha-Dunghu J, et al. J Cell Sci, 2008 May 15. PMID 18445686

See all (62) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Bi-allelic variants in SPATA5L1 lead to intellectual disability, spastic-dystonic cerebral palsy, epilepsy, and hearing loss.
    Title: Bi-allelic variants in SPATA5L1 lead to intellectual disability, spastic-dystonic cerebral palsy, epilepsy, and hearing loss.
  2. Observational study, meta-analysis, and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Multiple loci associated with indices of renal function and chronic kidney disease.
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

Associated conditions

Description Tests
Hearing loss, autosomal recessive 119
MedGen: C5562023 OMIM: 619615 GeneReviews: Not available
Compare labs
Neurodevelopmental disorder with hearing loss and spasticity
MedGen: C5562024 OMIM: 619616 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Multiple loci associated with indices of renal function and chronic kidney disease.
EBI GWAS Catalog
New loci associated with kidney function and chronic kidney disease.
EBI GWAS Catalog
Using multiple measures for quantitative trait association analyses: application to estimated glomerular filtration rate.
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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Pr55(Gag) gag Interaction of HIV-1 Gag with spermatogenesis associated 5-like 1 (SPATA5L1) is identified in a series of six affinity purification/mass spectrometry screens PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC5347, FLJ12286

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 ribosomal large subunit biogenesis IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus 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 B
Names
ribosome biogenesis protein SPATA5L1
spermatogenesis associated 5 like 1
spermatogenesis-associated protein 5-like protein 1
NP_001310569.1
NP_076968.2

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.

mRNA and Protein(s)

  1. NM_001323640.2 → NP_001310569.1  ATPase family gene 2 protein homolog B isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC025580
    Consensus CDS
    CCDS81877.1
    UniProtKB/Swiss-Prot
    Q9BVQ7
    Related
    ENSP00000436823.1, ENST00000531970.5
    Conserved Domains (3) summary
    smart00382
    Location:234 → 370
    AAA; ATPases associated with a variety of cellular activities
    COG1222
    Location:446 → 596
    RPT1; ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
    pfam00004
    Location:237 → 367
    AAA; ATPase family associated with various cellular activities (AAA)

  2. NM_024063.3 → NP_076968.2  ATPase family gene 2 protein homolog B isoform 1

    See identical proteins and their annotated locations for NP_076968.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript and encodes the functional protein.
    Source sequence(s)
    AA451905, AC025580, AK225463, DC346759
    Consensus CDS
    CCDS10123.1
    UniProtKB/Swiss-Prot
    C9JHR5, Q9BVQ7, Q9H8W7, Q9HA41
    Related
    ENSP00000305494.6, ENST00000305560.11
    Conserved Domains (2) summary
    TIGR01243
    Location:22 → 746
    CDC48; AAA family ATPase, CDC48 subfamily
    pfam00004
    Location:501 → 651
    AAA; ATPase family associated with various cellular activities (AAA)

RNA

  1. NR_027635.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AA451905, AC025580, AK023232

  2. NR_136645.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC025580

  3. NR_136646.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC025580

  4. NR_136647.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC025580

  5. NR_136648.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC025580

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    45402336..45421415
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    43210511..43229587
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BVQ7.2 GenPept UniProtKB/Swiss-Prot:Q9BVQ7

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
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