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HFM1 Gene(Protein Coding)

HFM1, ATP Dependent DNA Helicase Homolog

GCID:
GC01M091260
GIFtS:
51
Genes Participants
UDN Logo

Aliases for HFM1 Gene

Aliases for HFM1 Gene

  • HFM1, ATP Dependent DNA Helicase Homolog 2 3 5
  • SEC63 Domain-Containing Protein 1 3 4
  • HFM1, ATP-Dependent DNA Helicase Homolog (S. Cerevisiae) 2
  • Probable ATP-Dependent DNA Helicase HFM1 3
  • Helicase-Like Protein HFM1 3
  • SEC63 Domain Containing 1 2
  • EC 3.6.4.12 4
  • Helicase 3
  • EC 3.6.1 61
  • Si-11-6 3
  • SEC63D1 3
  • SEC3D1 4
  • Si-11 3
  • MER3 3
  • POF9 3

External Ids for HFM1 Gene

Previous HGNC Symbols for HFM1 Gene

  • SEC63D1

Previous GeneCards Identifiers for HFM1 Gene

  • GC01M091556
  • GC01M091499
  • GC01M091726
  • GC01M089845

Summaries for HFM1 Gene

Entrez Gene Summary for HFM1 Gene

  • The protein encoded by this gene is thought to be an ATP-dependent DNA helicase and is expressed mainly in germ-line cells. Defects in this gene are a cause of premature ovarian failure 9 (POF9). [provided by RefSeq, Apr 2014]

GeneCards Summary for HFM1 Gene

HFM1 (HFM1, ATP Dependent DNA Helicase Homolog) is a Protein Coding gene. Diseases associated with HFM1 include Premature Ovarian Failure 9 and Spastic Hemiplegia. GO annotations related to this gene include nucleic acid binding and helicase activity.

UniProtKB/Swiss-Prot for HFM1 Gene

  • Required for crossover formation and complete synapsis of homologous chromosomes during meiosis.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HFM1 Gene

Genomics for HFM1 Gene

Products:

  1. Regulatory Element

Regulatory Elements for HFM1 Gene

Enhancers for HFM1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01G091403 1 ENCODE 26.4 +3.4 3393 1.4 HDGF FOXA2 CREB3L1 ARNT ARID4B DMAP1 ZNF2 ZNF766 CBX5 SP3 HFM1 GC01P091329
GH01G091882 1.4 ENCODE dbSUPER 9.5 -477.0 -477033 4.4 PKNOX1 FOXA2 CREB3L1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 SNORA66 SNORD21 RPL5 TGFBR3 HFM1 GLMN GC01M091855
GH01G091499 1.1 ENCODE 10.5 -93.6 -93567 3.4 HDGF HNRNPUL1 CREB3L1 ARNT AGO1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 CDC7 HFM1 GC01P091527
GH01G091530 0.9 Ensembl dbSUPER 9.8 -122.1 -122094 0.2 CTCF ZNF654 NR4A1 MAFG ELF1 REST RAD21 ZNF366 SMC3 NFE2 HFM1 WDR82P2 GC01M091533 GC01P091527
GH01G091165 0.8 ENCODE 10.5 +242.6 242579 0.2 BCOR HDGF CTCF ZNF146 RB1 TAL1 ZMYM3 RAD21 ARID3A GATA2 HFM1 GC01M091130 PIR32329
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HFM1 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the HFM1 gene promoter:

Genomic Location for HFM1 Gene

Chromosome:
1
Start:
91,260,766 bp from pter
End:
91,408,007 bp from pter
Size:
147,242 bases
Orientation:
Minus strand

Genomic View for HFM1 Gene

Genes around HFM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HFM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HFM1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for HFM1 Gene

Proteins for HFM1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for HFM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A2PYH4-HFM1_HUMAN
    Recommended name:
    Probable ATP-dependent DNA helicase HFM1
    Protein Accession:
    A2PYH4
    Secondary Accessions:
    • B1B0B6
    • Q8N9Q0

    Protein attributes for HFM1 Gene

    Size:
    1435 amino acids
    Molecular mass:
    162610 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for HFM1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HFM1 Gene

Protein Expression for HFM1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for HFM1 Gene

A2PYH4:
  • QMIGRAGR
  • APTGSGKT
  • GRAGRPQF

Post-translational modifications for HFM1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HFM1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for HFM1 Gene

Gene Families for HFM1 Gene

HGNC:

Protein Domains for HFM1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for HFM1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

A2PYH4

UniProtKB/Swiss-Prot:

HFM1_HUMAN :
  • Belongs to the helicase family. SKI2 subfamily.
Family:
  • Belongs to the helicase family. SKI2 subfamily.
genes like me logo Genes that share domains with HFM1: view

Function for HFM1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for HFM1 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.
UniProtKB/Swiss-Prot Function:
Required for crossover formation and complete synapsis of homologous chromosomes during meiosis.

Enzyme Numbers (IUBMB) for HFM1 Gene

Gene Ontology (GO) - Molecular Function for HFM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0004004 ATP-dependent RNA helicase activity IBA --
GO:0004386 helicase activity IEA --
GO:0005524 ATP binding IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with HFM1: view
genes like me logo Genes that share phenotypes with HFM1: view

Human Phenotype Ontology for HFM1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for HFM1 Gene

Localization for HFM1 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HFM1 gene
Compartment Confidence
nucleus 4
cytosol 2

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for HFM1 Gene

Pathways & Interactions for HFM1 Gene

SuperPathways for HFM1 Gene

PathCards logo More details on SuperPathways for HFM1
No Data Available

Interacting Proteins for HFM1 Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000359454%0d%0a9606.ENSP00000266079%0d%0a9606.ENSP00000222969%0d%0a9606.ENSP00000304370%0d%0a9606.ENSP00000227524%0d%0a9606.ENSP00000360532%0d%0a
Selected Interacting proteins: ENSP00000359454 for HFM1 Gene via STRING

Gene Ontology (GO) - Biological Process for HFM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000712 resolution of meiotic recombination intermediates IEA --
GO:0010501 RNA secondary structure unwinding IBA --
GO:0051321 meiotic cell cycle IEA --
genes like me logo Genes that share ontologies with HFM1: view

No data available for Pathways by source and SIGNOR curated interactions for HFM1 Gene

Drugs & Compounds for HFM1 Gene

Products:

  1. Drug

(3) Drugs for HFM1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
Adenosine triphosphate Approved Nutra 0

(1) Additional Compounds for HFM1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
 Full agonist, Agonist 58-64-0
genes like me logo Genes that share compounds with HFM1: view

Transcripts for HFM1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for HFM1 Gene

(15) REFSEQ mRNAs :
(13) Additional mRNA sequences :
(2) Selected AceView cDNA sequences:
(9) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HFM1 Gene

HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for HFM1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20
SP1: -
SP2:

Relevant External Links for HFM1 Gene

GeneLoc Exon Structure for
HFM1
ECgene alternative splicing isoforms for
HFM1

Expression for HFM1 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HFM1 Gene

mRNA expression in normal human tissues for HFM1 Gene
mRNA expression by GTEx for HFM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HFM1 Gene

This gene is overexpressed in Pituitary (x12.1) and Testis (x6.9).

Protein differential expression in normal tissues from HIPED for HFM1 Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (60.3) and Pancreatic juice (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for HFM1 Gene



Protein tissue co-expression partners for HFM1 Gene

NURSA nuclear receptor signaling pathways regulating expression of HFM1 Gene:

HFM1

SOURCE GeneReport for Unigene cluster for HFM1 Gene:

Hs.454818

mRNA Expression by UniProt/SwissProt for HFM1 Gene:

A2PYH4-HFM1_HUMAN
Tissue specificity: Preferentially expressed in testis and ovary.

Phenotype-based relationships between genes and organs from Gene ORGANizer for HFM1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • endocrine
  • integumentary
  • nervous
  • reproductive
Organs:
Head and neck:
  • brain
  • head
  • pituitary gland
Thorax:
  • breast
Pelvis:
  • fallopian tube
  • ovary
  • penis
  • prostate
  • testicle
  • uterus
  • vagina
  • vulva
General:
  • hair
  • skin
genes like me logo Genes that share expression patterns with HFM1: view

Primer Products

No data available for Evidence on tissue expression from TISSUES for HFM1 Gene

Orthologs for HFM1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HFM1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia HFM1 34 35
  • 99.54 (n)
dog
(Canis familiaris)
 Mammalia HFM1 34 35
  • 90.72 (n)
cow
(Bos Taurus)
 Mammalia HFM1 34 35
  • 90.39 (n)
mouse
(Mus musculus)
 Mammalia Hfm1 34 16 35
  • 83.16 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia -- 35
  • 83 (a)
 OneToMany
-- 35
  • 69 (a)
 OneToMany
-- 35
  • 49 (a)
 OneToMany
rat
(Rattus norvegicus)
 Mammalia Hfm1 34
  • 81.74 (n)
oppossum
(Monodelphis domestica)
 Mammalia HFM1 35
  • 70 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves HFM1 34
  • 70.06 (n)
-- 35
  • 66 (a)
 OneToMany
-- 35
  • 56 (a)
 OneToMany
lizard
(Anolis carolinensis)
 Reptilia HFM1 35
  • 62 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia hfm1 34
  • 64.71 (n)
zebrafish
(Danio rerio)
 Actinopterygii hfm1 34 35
  • 62.56 (n)
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP009060 34
  • 45 (n)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes HFM1 35
  • 28 (a)
 OneToOne
thale cress
(Arabidopsis thaliana)
 eudicotyledons RCK 34
  • 50.79 (n)
rice
(Oryza sativa)
 Liliopsida Os02g0617500 34
  • 52.29 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea -- 35
  • 56 (a)
 OneToOne
Species where no ortholog for HFM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HFM1 Gene

ENSEMBL:
Gene Tree for HFM1 (if available)
TreeFam:
Gene Tree for HFM1 (if available)

Paralogs for HFM1 Gene

(2) SIMAP similar genes for HFM1 Gene using alignment to 8 proteins:

genes like me logo Genes that share paralogs with HFM1: view

No data available for Paralogs for HFM1 Gene

Variants for HFM1 Gene

Sequence variations from dbSNP and Humsavar for HFM1 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs587777268 Pathogenic, Premature ovarian failure 9 (POF9) [MIM:615724] 91,319,322(+) TGAAA(A/C)TCTTT intron-variant, nc-transcript-variant, reference, missense, utr-variant-3-prime
rs587777269 Pathogenic, Premature ovarian failure 9 (POF9) [MIM:615724] 91,350,738(+) CAAAC(C/T)ATAAT nc-transcript-variant, reference, missense
rs587777270 Pathogenic 91,266,061(+) TGAAG(C/GG)GTAGC intron-variant, reference, frameshift-variant
rs730880018 Pathogenic 91,353,299(+) TGTAA(C/G)CTATT nc-transcript-variant, reference, missense
rs1000059385 -- 91,363,874(+) TATCA(C/T)GTCCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for HFM1 Gene

Variant ID Type Subtype PubMed ID
dgv1n35 CNV novel sequence insertion 20440878
esv2714684 CNV deletion 23290073
esv3586790 CNV gain 21293372
esv5793 CNV gain 19470904
esv6422 CNV gain 19470904
nsv1006022 CNV loss 25217958
nsv1113148 CNV deletion 24896259
nsv1137780 CNV deletion 24896259
nsv1137781 CNV deletion 24896259
nsv437904 CNV loss 16468122
nsv472327 CNV novel sequence insertion 20440878
nsv473544 CNV novel sequence insertion 20440878
nsv475265 CNV novel sequence insertion 20440878
nsv475363 CNV novel sequence insertion 20440878
nsv479129 CNV novel sequence insertion 20440878
nsv480471 CNV novel sequence insertion 20440878
nsv519110 CNV loss 19592680
nsv546806 CNV loss 21841781
nsv946067 CNV duplication 23825009

Variation tolerance for HFM1 Gene

Residual Variation Intolerance Score: 6.16% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.84; 73.96% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HFM1 Gene

Human Gene Mutation Database (HGMD)
HFM1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HFM1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HFM1 Gene

Disorders for HFM1 Gene

MalaCards: The human disease database

(7) MalaCards diseases for HFM1 Gene - From: OMIM, ClinVar, GeneTests, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
premature ovarian failure 9
  • pof9
spastic hemiplegia
  • congenital hemiplegia
periarthritis
premature ovarian failure
  • premature menopause
epicondylitis
  • andrel epicondylitis
- elite association - COSMIC cancer census association via MalaCards
Search HFM1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

HFM1_HUMAN
  • Premature ovarian failure 9 (POF9) [MIM:615724]: An ovarian disorder defined as the cessation of ovarian function under the age of 40 years. It is characterized by oligomenorrhea or amenorrhea, in the presence of elevated levels of serum gonadotropins and low estradiol. {ECO:0000303 PubMed:24597873}. Note=The disease may be caused by mutations affecting the gene represented in this entry.

Relevant External Links for HFM1

Genetic Association Database (GAD)
HFM1
Human Genome Epidemiology (HuGE) Navigator
HFM1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HFM1
genes like me logo Genes that share disorders with HFM1: view

No data available for Genatlas for HFM1 Gene

Publications for HFM1 Gene

  1. HFM1, the human homologue of yeast Mer3, encodes a putative DNA helicase expressed specifically in germ-line cells. (PMID: 17286053) Tanaka K. … Ikeda J.E. (DNA Seq. 2006) 2 3 4 22 64
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 2 3 4 64
  3. Mutations in HFM1 in recessive primary ovarian insufficiency. (PMID: 24597873) Wang J. … Wu B.L. (N. Engl. J. Med. 2014) 3 4 64
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  5. Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study. (PMID: 20800603) Flachsbart F. … Nebel A. (Mutat. Res. 2010) 3 46 64

Products for HFM1 Gene

Sources for HFM1 Gene

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