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HMCES 5-hydroxymethylcytosine binding, ES cell specific [ Homo sapiens (human) ]

Gene ID: 56941, updated on 25-Nov-2025
Official Symbol
HMCESprovided by HGNC
Official Full Name
5-hydroxymethylcytosine binding, ES cell specificprovided by HGNC
Primary source
HGNC:HGNC:24446
See related
Ensembl:ENSG00000183624 MIM:618288; AllianceGenome:HGNC:24446
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
DC12; SRAPD1; C3orf37
Summary
Enables DNA-(abasic site) binding activity; protein-DNA covalent cross-linking activity; and single-stranded DNA binding activity. Involved in interstrand cross-link repair; protein-DNA covalent cross-linking repair; and somatic hypermutation of immunoglobulin genes. Is active in replication fork. [provided by Alliance of Genome Resources, Jul 2025]
Expression
Ubiquitous expression in lymph node (RPKM 40.1), testis (RPKM 20.9) and 24 other tissues See more
Orthologs
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See HMCES in Genome Data Viewer
Location:
3q21.3
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2025_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (129278832..129306186)
RS_2025_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (132023631..132050984)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (128997675..129025029)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374102 Neighboring gene NANOG hESC enhancer GRCh37_chr3:128950251-128950752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20507 Neighboring gene CRISPRi-FlowFISH-validated H1-10 regulatory element 3 Neighboring gene coat protein complex I subunit gamma 1 Neighboring gene microRNA 6826 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14719 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20508 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:129024401-129024985 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20509 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14721 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14722 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14723 Neighboring gene H1-10 antisense RNA 1 Neighboring gene H1.10 linker histone Neighboring gene nucleoporin 210 pseudogene 3

Go to nucleotide: Graphics FASTA GenBank

  • 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

Related articles in PubMed

  1. Cross-region reduction in 5-hydroxymethylcytosine in Alzheimer's disease brain. Condliffe D, et al. Neurobiol Aging, 2014 Aug. PMID 24679604, Free PMC Article
  2. A non-proteolytic release mechanism for HMCES-DNA-protein crosslinks. Donsbach M, et al. EMBO J, 2023 Sep 18. PMID 37519246, Free PMC Article
  3. Self-reversal facilitates the resolution of HMCES DNA-protein crosslinks in cells. Rua-Fernandez J, et al. Cell Rep, 2023 Nov 28. PMID 37950866, Free PMC Article
  4. Characterization of global 5-hydroxymethylcytosine in pediatric posterior fossa ependymoma. Wu T, et al. Clin Epigenetics, 2020 Jan 28. PMID 31992357, Free PMC Article
  5. HMCES safeguards replication from oxidative stress and ensures error-free repair. Srivastava M, et al. EMBO Rep, 2020 Jun 4. PMID 32307824, Free PMC Article

See all (48) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 5-Hydroxymethylation highlights the heterogeneity in keratinization and cell junctions in head and neck cancers.
    Title: 5-Hydroxymethylation highlights the heterogeneity in keratinization and cell junctions in head and neck cancers.
  2. Loss of the abasic site sensor HMCES is synthetic lethal with the activity of the APOBEC3A cytosine deaminase in cancer cells.
    Title: Loss of the abasic site sensor HMCES is synthetic lethal with the activity of the APOBEC3A cytosine deaminase in cancer cells.
  3. Characterization of global 5-hydroxymethylcytosine in pediatric posterior fossa ependymoma.
    Title: Characterization of global 5-hydroxymethylcytosine in pediatric posterior fossa ependymoma.
  4. HMCES Maintains Replication Fork Progression and Prevents Double-Strand Breaks in Response to APOBEC Deamination and Abasic Site Formation.
    Title: HMCES Maintains Replication Fork Progression and Prevents Double-Strand Breaks in Response to APOBEC Deamination and Abasic Site Formation.
  5. HMCES safeguards replication from oxidative stress and ensures error-free repair.
    Title: HMCES safeguards replication from oxidative stress and ensures error-free repair.
  6. Structural biology of DNA abasic site protection by SRAP proteins.
    Title: Structural biology of DNA abasic site protection by SRAP proteins.
  7. This study reports crystal structures of the human HMCES SOS response-associated peptidase (SRAP) domain in complex with DNA-damage substrates, including HMCES cross-linked with an abasic site within a 3' overhang DNA.
    Title: Structural basis of HMCES interactions with abasic DNA and multivalent substrate recognition.
  8. The findings of this study described in this study emphasise the importance of 5hmC in brain development and ageing and will help to better understand the complexity and plasticity of the brain.
    Title: 5-Hydroxymethylcytosine, the "Sixth Base", during brain development and ageing.
  9. 5-hmC might be involved in the pathogenesis of Nonalcoholic Fatty Liver Disease by regulating liver mitochondrial biogenesis and PPARGC1A expression.
    Title: Epigenetic Modifications in the Biology of Nonalcoholic Fatty Liver Disease: The Role of DNA Hydroxymethylation and TET Proteins.
  10. The expression of 5-hmC was an independent prognostic factor for overall survival of EOC [epithelial ovarian canc] patients.
    Title: Prognostic values of 5-hmC, 5-mC and TET2 in epithelial ovarian cancer.
Submit: New GeneRIF Correction See all GeneRIFs (12)

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

Review eQTL and phenotype association data in this region using PheGenI

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • MGC111075

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-(abasic site) binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-(abasic site) binding IDA
Inferred from Direct Assay
more info
 PubMed 
NOT enables DNA-(apurinic or apyrimidinic site) endonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables lyase activity IEA
Inferred from Electronic Annotation
more info
  
enables peptidase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-DNA covalent cross-linking activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein-DNA covalent cross-linking activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables single-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables single-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables single-stranded DNA binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in DNA damage response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in DNA damage response IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA repair IEA
Inferred from Electronic Annotation
more info
  
involved_in double-strand break repair via alternative nonhomologous end joining IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in double-strand break repair via alternative nonhomologous end joining IEA
Inferred from Electronic Annotation
more info
  
involved_in interstrand cross-link repair IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in interstrand cross-link repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of isotype switching IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of isotype switching ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein-DNA covalent cross-linking repair IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein-DNA covalent cross-linking repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein-DNA covalent cross-linking repair IEA
Inferred from Electronic Annotation
more info
  
involved_in proteolysis IEA
Inferred from Electronic Annotation
more info
  
involved_in somatic hypermutation of immunoglobulin genes IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in somatic hypermutation of immunoglobulin genes IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in somatic hypermutation of immunoglobulin genes IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in chromosome IEA
Inferred from Electronic Annotation
more info
  
is_active_in replication fork IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in replication fork IDA
Inferred from Direct Assay
more info
 PubMed 
Preferred Names
abasic site processing protein HMCES
Names
5-hydroxymethylcytosine (hmC) binding, ES cell-specific
ES cell-specific 5hmC-binding protein
SOS response associated peptidase domain containing 1
SRAP domain-containing protein 1
UPF0361 protein C3orf37
embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein
peptidase HMCES
putative endonuclease HMCES
putative peptidase SRAPD1

NEW Try the new Transcript table

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_001006109.1 → NP_001006109.1  abasic site processing protein HMCES isoform a

    See identical proteins and their annotated locations for NP_001006109.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    BC050686, BU728549
    Consensus CDS
    CCDS33852.1
    UniProtKB/Swiss-Prot
    A6NJR9, Q96FZ2, Q96G34, Q9NRP3
    UniProtKB/TrEMBL
    B4DMK2
    Related
    ENSP00000374385.3, ENST00000389735.7
    Conserved Domains (1) summary
    pfam02586
    Location:1 → 259
    SRAP; SOS response associated peptidase (SRAP)

  2. NM_001363881.1 → NP_001350810.1  abasic site processing protein HMCES isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AC137695
    Consensus CDS
    CCDS87134.1
    UniProtKB/TrEMBL
    B4DMK2, E7EMP6
    Related
    ENSP00000392966.2, ENST00000417226.6
    Conserved Domains (1) summary
    cl03646
    Location:31 → 230
    SRAP; SOS response associated peptidase (SRAP)

  3. NM_001370343.1 → NP_001357272.1  abasic site processing protein HMCES isoform a

    Status: VALIDATED

    Source sequence(s)
    AC137695, AK025883, BC009993, CN335364
    Consensus CDS
    CCDS33852.1
    UniProtKB/Swiss-Prot
    A6NJR9, Q96FZ2, Q96G34, Q9NRP3
    UniProtKB/TrEMBL
    B4DMK2
    Related
    ENSP00000426215.1, ENST00000502878.6
    Conserved Domains (1) summary
    pfam02586
    Location:1 → 259
    SRAP; SOS response associated peptidase (SRAP)

  4. NM_001370344.1 → NP_001357273.1  abasic site processing protein HMCES isoform a

    Status: VALIDATED

    Source sequence(s)
    AC137695, BC009993, BE790516
    Consensus CDS
    CCDS33852.1
    UniProtKB/Swiss-Prot
    A6NJR9, Q96FZ2, Q96G34, Q9NRP3
    UniProtKB/TrEMBL
    B4DMK2
    Conserved Domains (1) summary
    pfam02586
    Location:1 → 259
    SRAP; SOS response associated peptidase (SRAP)

  5. NM_001370345.1 → NP_001357274.1  abasic site processing protein HMCES isoform c

    Status: VALIDATED

    Source sequence(s)
    AC137695
    UniProtKB/TrEMBL
    D6R9T3
    Related
    ENSP00000423132.1, ENST00000509042.5
    Conserved Domains (1) summary
    pfam02586
    Location:1 → 211
    SRAP; SOS response associated peptidase (SRAP)

  6. NM_020187.3 → NP_064572.2  abasic site processing protein HMCES isoform a

    See identical proteins and their annotated locations for NP_064572.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AC137695, AF201934, BC010125
    Consensus CDS
    CCDS33852.1
    UniProtKB/Swiss-Prot
    A6NJR9, Q96FZ2, Q96G34, Q9NRP3
    UniProtKB/TrEMBL
    B4DMK2
    Related
    ENSP00000372955.3, ENST00000383463.9
    Conserved Domains (1) summary
    pfam02586
    Location:1 → 259
    SRAP; SOS response associated peptidase (SRAP)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    129278832..129306186
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    132023631..132050984
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96FZ2.1 GenPept UniProtKB/Swiss-Prot:Q96FZ2

Gene LinkOut

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