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RNF212 ring finger protein 212 [ Homo sapiens (human) ]

Gene ID: 285498, updated on 5-Mar-2024

Summary

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Official Symbol
RNF212provided by HGNC
Official Full Name
ring finger protein 212provided by HGNC
Primary source
HGNC:HGNC:27729
See related
Ensembl:ENSG00000178222 MIM:612041; AllianceGenome:HGNC:27729
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
ZHP3; SPGF62
Summary
This gene encodes a RING finger protein that may function as a ubiquitin ligase. The encoded protein may be involved in meiotic recombination. This gene is located within a linkage disequilibrium block and polymorphisms in this gene may influence recombination rates. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Oct 2010]
Expression
Broad expression in ovary (RPKM 1.7), testis (RPKM 1.5) and 20 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
4p16.3
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (1056251..1113710, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (1055136..1112433, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (1050039..1107352, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1003737-1004369 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15120 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15121 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1007938-1008741 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1008742-1009544 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1011927-1012796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1019533-1020034 Neighboring gene fibroblast growth factor receptor like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1020035-1020534 Neighboring gene uncharacterized LOC105374343 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1030079-1030899 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1032665-1033598 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:1035128-1035326 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:1035707-1035888 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1046553-1047422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1085059-1086038 Neighboring gene protein phosphatase 2 regulatory subunit B, alpha pseudogene Neighboring gene uncharacterized LOC105374344 Neighboring gene nascent polypeptide-associated complex subunit alpha, muscle-specific form-like Neighboring gene small nucleolar RNA SNORA48 Neighboring gene transmembrane p24 trafficking protein 11, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15122 Neighboring gene hornerin-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1143546-1144046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1144047-1144547

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. Association of the common SNPs in RNF212, STAG3 and RFX2 gene with male infertility with azoospermia in Chinese population. Yu CH, et al. Eur J Obstet Gynecol Reprod Biol, 2018 Feb. PMID 29277047
  2. Sequencing of a 'mouse azoospermia' gene panel in azoospermic men: identification of RNF212 and STAG3 mutations as novel genetic causes of meiotic arrest. Riera-Escamilla A, et al. Hum Reprod, 2019 Jun 4. PMID 31125047
  3. Genetic analysis of variation in human meiotic recombination. Chowdhury R, et al. PLoS Genet, 2009 Sep. PMID 19763160, Free PMC Article
  4. Sequence variants in the RNF212 gene associate with genome-wide recombination rate. Kong A, et al. Science, 2008 Mar 7. PMID 18239089
  5. Targeted gene knockout reveals a role in meiotic recombination for ZHP-3, a Zip3-related protein in Caenorhabditis elegans. Jantsch V, et al. Mol Cell Biol, 2004 Sep. PMID 15340062, Free PMC Article

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. For the first time, study reports biallelic variants in STAG3, in one sporadic patient, and a homozygous RNF212 variant, in the two brothers, as the genetic cause of non-obstructive azoospermia. Meiotic studies allowed the detection of the functional consequences of the mutations and provided information on the role of STAG3 and RNF212 in human male meiosis.
    Title: Sequencing of a 'mouse azoospermia' gene panel in azoospermic men: identification of RNF212 and STAG3 mutations as novel genetic causes of meiotic arrest.
  2. The polymorphism of SNP rs4045481 in RNF212 gene might be associated with azoospermia and genotype CC of this SNP may be a risk factor of azoospermia.
    Title: Association of the common SNPs in RNF212, STAG3 and RFX2 gene with male infertility with azoospermia in Chinese population.
  3. This paper describes a partial transcript of the human RNF212 gene.
    Title: Targeted gene knockout reveals a role in meiotic recombination for ZHP-3, a Zip3-related protein in Caenorhabditis elegans.
  4. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Sequence variants in the RNF212 gene associate with genome-wide recombination rate.
  5. genome search identified sequence variants in the 4p16.3 region correlated with recombination rate in males & females; variants are located in the RNF212 gene, a putative ortholog of ZHP-3 gene essential for recombination & chiasma formation in C elegans
    Title: Sequence variants in the RNF212 gene associate with genome-wide recombination rate.
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
Recombination rate quantitative trait locus 1
MedGen: C2677576 OMIM: 612042 GeneReviews: Not available
Compare labs
Spermatogenic failure 62
MedGen: C5562049 OMIM: 619673 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
Sequence variants in the RNF212 gene associate with genome-wide recombination 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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ38841, FLJ42587, MGC120227, MGC120228

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables SUMO transferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in chiasma assembly ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in homologous chromosome pairing at meiosis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in meiotic gene conversion ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein sumoylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein sumoylation IEA
Inferred from Electronic Annotation
more info
  
involved_in reciprocal meiotic recombination ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
is_active_in synaptonemal complex IBA
Inferred from Biological aspect of Ancestor
more info
  
colocalizes_with synaptonemal complex ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
probable E3 SUMO-protein ligase RNF212
Names
probable E3 SUMO-protein transferase RNF212

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_027812.2 RefSeqGene

    Range
    5231..47317
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001131034.4 → NP_001124506.1  probable E3 SUMO-protein ligase RNF212 isoform a

    See identical proteins and their annotated locations for NP_001124506.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC019103, AK096160, BC050356, BC101260, BG701603
    Consensus CDS
    CCDS46996.1
    UniProtKB/Swiss-Prot
    C9J8N0, Q495C0, Q495C1, Q86W82, Q8IY99, Q8N8U7
    Related
    ENSP00000389709.2, ENST00000433731.7
    Conserved Domains (1) summary
    cl17238
    Location:4 → 50
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

  2. NM_001193318.3 → NP_001180247.1  probable E3 SUMO-protein ligase RNF212 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks multiple 3' exons but has an alternate 3' exon, compared to variant 1. The resulting isoform (c) is shorter and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AC019103, AK096160, BC036250, BG701603
    Consensus CDS
    CCDS54704.1
    UniProtKB/Swiss-Prot
    Q495C1
    Related
    ENSP00000327481.5, ENST00000333673.5
    Conserved Domains (1) summary
    pfam14634
    Location:6 → 47
    zf-RING_5; zinc-RING finger domain

  3. NM_001366918.1 → NP_001353847.1  probable E3 SUMO-protein ligase RNF212 isoform d

    Status: REVIEWED

    Source sequence(s)
    AC019103, AC092535

  4. NM_001366919.1 → NP_001353848.1  probable E3 SUMO-protein ligase RNF212 isoform e

    Status: REVIEWED

    Source sequence(s)
    AC019103, AC092535
    Consensus CDS
    CCDS93460.1
    UniProtKB/TrEMBL
    A0A8V8TN20
    Related
    ENSP00000513634.1, ENST00000698262.1
    Conserved Domains (1) summary
    cd16746
    Location:4 → 50
    RING-HC_RNF212; RING finger, HC subclass, found in RING finger protein 212 (RNF212) and similar proteins

  5. NM_194439.5 → NP_919420.1  probable E3 SUMO-protein ligase RNF212 isoform b

    See identical proteins and their annotated locations for NP_919420.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, compared to variant 1, that results in a frameshift. It encodes isoform b which has a shorter and distinct C-terminus compared to isoform a.
    Source sequence(s)
    AC019103, AK096160, BC050356, BG701603
    Consensus CDS
    CCDS3345.1
    UniProtKB/Swiss-Prot
    Q495C1
    Related
    ENSP00000372428.5, ENST00000382968.9
    Conserved Domains (1) summary
    pfam14634
    Location:6 → 47
    zf-RING_5; zinc-RING finger domain

RNA

  1. NR_159497.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC019103, AC092535

  2. NR_159498.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC019103, AC092535

  3. NR_159499.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC019103, AC092535

  4. NR_159500.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC019103, AC092535

  5. NR_159501.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC019103, AC092535

  6. NR_159502.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC019103, AC092535

  7. NR_159503.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC019103, AC092535

  8. NR_159504.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC019103, AC092535

  9. NR_159505.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC019103, AC092535

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
    1056251..1113710 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011513446.2 → XP_011511748.1  probable E3 SUMO-protein ligase RNF212 isoform X9

    Conserved Domains (1) summary
    pfam14634
    Location:6 → 47
    zf-RING_5; zinc-RING finger domain

  2. XM_047450083.1 → XP_047306039.1  probable E3 SUMO-protein ligase RNF212 isoform X3

  3. XM_047450082.1 → XP_047306038.1  probable E3 SUMO-protein ligase RNF212 isoform X1

  4. XM_047450084.1 → XP_047306040.1  probable E3 SUMO-protein ligase RNF212 isoform X4

  5. XM_017008040.2 → XP_016863529.1  probable E3 SUMO-protein ligase RNF212 isoform X2

  6. XM_011513445.3 → XP_011511747.1  probable E3 SUMO-protein ligase RNF212 isoform X6

    Conserved Domains (1) summary
    pfam14634
    Location:6 → 47
    zf-RING_5; zinc-RING finger domain

  7. XM_047450086.1 → XP_047306042.1  probable E3 SUMO-protein ligase RNF212 isoform X7

  8. XM_011513439.2 → XP_011511741.1  probable E3 SUMO-protein ligase RNF212 isoform X2

    See identical proteins and their annotated locations for XP_011511741.1

  9. XM_047450085.1 → XP_047306041.1  probable E3 SUMO-protein ligase RNF212 isoform X5

  10. XM_047450087.1 → XP_047306043.1  probable E3 SUMO-protein ligase RNF212 isoform X8

  11. XM_047450088.1 → XP_047306044.1  probable E3 SUMO-protein ligase RNF212 isoform X10

  12. XM_017008041.2 → XP_016863530.1  probable E3 SUMO-protein ligase RNF212 isoform X11

RNA

  1. XR_007096392.1 RNA Sequence

  2. XR_924937.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    1055136..1112433 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054349724.1 → XP_054205699.1  probable E3 SUMO-protein ligase RNF212 isoform X9

  2. XM_054349718.1 → XP_054205693.1  probable E3 SUMO-protein ligase RNF212 isoform X3

  3. XM_054349715.1 → XP_054205690.1  probable E3 SUMO-protein ligase RNF212 isoform X1

  4. XM_054349719.1 → XP_054205694.1  probable E3 SUMO-protein ligase RNF212 isoform X4

  5. XM_054349717.1 → XP_054205692.1  probable E3 SUMO-protein ligase RNF212 isoform X2

  6. XM_054349721.1 → XP_054205696.1  probable E3 SUMO-protein ligase RNF212 isoform X6

  7. XM_054349722.1 → XP_054205697.1  probable E3 SUMO-protein ligase RNF212 isoform X7

  8. XM_054349716.1 → XP_054205691.1  probable E3 SUMO-protein ligase RNF212 isoform X2

  9. XM_054349720.1 → XP_054205695.1  probable E3 SUMO-protein ligase RNF212 isoform X5

  10. XM_054349723.1 → XP_054205698.1  probable E3 SUMO-protein ligase RNF212 isoform X8

  11. XM_054349725.1 → XP_054205700.1  probable E3 SUMO-protein ligase RNF212 isoform X10

RNA

  1. XR_008486966.1 RNA Sequence

  2. XR_008486965.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q495C1.1 GenPept UniProtKB/Swiss-Prot:Q495C1

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