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

Gene ID: 79029, updated on 8-Mar-2025

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, Mar 2025]
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: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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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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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
not available
Neurodevelopmental disorder with hearing loss and spasticity
MedGen: C5562024 OMIM: 619616 GeneReviews: Not available
not available

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)

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 identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables polyubiquitin modification-dependent protein binding 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 autophagosome maturation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mitotic spindle disassembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in retrograde protein transport, ER to cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in ribosomal large subunit biogenesis IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of VCP-NPL4-UFD1 AAA ATPase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
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
Molecular Biology Databases
Research Materials
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