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EFHC2 EF-hand domain containing 2 [ Homo sapiens (human) ]

Gene ID: 80258, updated on 2-Nov-2024

Summary

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Official Symbol
EFHC2provided by HGNC
Official Full Name
EF-hand domain containing 2provided by HGNC
Primary source
HGNC:HGNC:26233
See related
Ensembl:ENSG00000183690 MIM:300817; AllianceGenome:HGNC:26233
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
MRX74; dJ1158H2.1
Summary
This gene encodes a protein which contains three DM10 domains and three calcium-binding EF-hand motifs. A related protein is encoded by a gene on chromosome 6. It has been suggested that both proteins are involved in the development of epilepsy (PMID: 15258581, 16112844) and that this gene may be associated with fear recognition in individuals with Turner syndrome. [provided by RefSeq, Aug 2011]
Expression
Broad expression in testis (RPKM 3.2), endometrium (RPKM 1.6) and 19 other tissues See more
Orthologs
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Genomic context

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See EFHC2 in Genome Data Viewer
Location:
Xp11.3
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (44147872..44343672, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (43554179..43750009, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (44007118..44202918, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:43808655-43809172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:43809173-43809689 Neighboring gene NDP antisense RNA 1 Neighboring gene norrin cystine knot growth factor NDP Neighboring gene RBM39 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20782 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:44111858-44112711 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:44112712-44113564 Neighboring gene Sharpr-MPRA regulatory region 13194 Neighboring gene TatD DNase domain containing 2 pseudogene 1 Neighboring gene ribonucleotide reductase M2 polypeptide pseudogene 3 Neighboring gene ubinuclein 1 pseudogene Neighboring gene farnesyl diphosphate synthase pseudogene 5

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. EFHC2 SNP rs7055196 is not associated with fear recognition in 45,X Turner syndrome. Zinn AR, et al. Am J Med Genet B Neuropsychiatr Genet, 2008 Jun 5. PMID 17948898
  2. Preliminary evidence of association between EFHC2, a gene implicated in fear recognition, and harm avoidance. Blaya C, et al. Neurosci Lett, 2009 Mar 6. PMID 19429002
  3. Identification of EFHC2 as a quantitative trait locus for fear recognition in Turner syndrome. Weiss LA, et al. Hum Mol Genet, 2007 Jan 1. PMID 17164267
  4. Variation in the X-linked EFHC2 gene is associated with social cognitive abilities in males. Startin CM, et al. PLoS One, 2015. PMID 26107779, Free PMC Article
  5. No relation between EFHC2 gene polymorphism and Idiopathic generalized epilepsy. Berrin T, et al. Afr Health Sci, 2015 Dec. PMID 26958022, Free PMC Article

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Our observations provide new information on the genotype-phenotype relations of MAOA/B and EFHC2 genes involved in the contiguous deletions of Norrie disease.Based on the case of our observation, contiguous deletion with only one of the MAO genes (MAOB) may not cause psychomotor disability, and deletion of EFHC2may not contribute to epilepsy.
    Title: A novel contiguous deletion involving NDP, MAOB and EFHC2 gene in a patient with familial Norrie disease: bilateral blindness and leucocoria without other deficits.
  2. In our series of 96 IGE patients and 96 healthy controls, there was no relation between S430Y polymorphism in EFHC2 gene and IGE presence.
    Title: No relation between EFHC2 gene polymorphism and Idiopathic generalized epilepsy.
  3. EFHC2 variation at SNP rs7055196 is associated with social cognitive abilities in males
    Title: Variation in the X-linked EFHC2 gene is associated with social cognitive abilities in males.
  4. This study found that the association between a variant in EFHC2 with the processing of fear and social threat and harm reduction.
    Title: Preliminary evidence of association between EFHC2, a gene implicated in fear recognition, and harm avoidance.
  5. no evidence of an association between rs7055196 genotype and fear recognition
    Title: EFHC2 SNP rs7055196 is not associated with fear recognition in 45,X Turner syndrome.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: Preliminary evidence of association between EFHC2, a gene implicated in fear recognition, and harm avoidance.
  7. An association with the gonosomal gene EFHC2 would be in accordance with the observed preponderance of maternal inheritance in juvenile myoclonic epilepsy maternal inheritance of juvenile myoclonic epilepsy.
    Title: A new EF-hand containing gene EFHC2 on Xp11.4: tentative evidence for association with juvenile myoclonic epilepsy.
  8. EFHC2 shows genealogy and extended LD consistent with directional selection. This novel QTL may influence social cognition in the general population and in autism.
    Title: Identification of EFHC2 as a quantitative trait locus for fear recognition in Turner syndrome.
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

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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Replication interactions

Interaction Pubs
Knockdown of EF-hand domain (C-terminal) containing 2 (EFHC2) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ22601, FLJ22843, DKFZp686G08235

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cellular response to leukemia inhibitory factor IEA
Inferred from Electronic Annotation
more info
  
involved_in flagellated sperm motility ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of neuron projection development IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in axonemal A tubule inner sheath ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in axonemal microtubule IDA
Inferred from Direct Assay
more info
 PubMed 
located_in axonemal microtubule ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in ciliary basal body IDA
Inferred from Direct Assay
more info
 PubMed 
colocalizes_with microtubule IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in sperm flagellum ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
EF-hand domain-containing family member C2
Names
EF-hand domain (C-terminal) containing 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.

Genomic

  1. NG_021391.2 RefSeqGene

    Range
    5000..200800
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_025184.4 → NP_079460.2  EF-hand domain-containing family member C2

    See identical proteins and their annotated locations for NP_079460.2

    Status: VALIDATED

    Source sequence(s)
    AC018719, AL133344, AL359744
    Consensus CDS
    CCDS55405.1
    UniProtKB/Swiss-Prot
    Q5JST6, Q5JST8, Q68DK4, Q8NEI0, Q9H653
    UniProtKB/TrEMBL
    A8K572
    Related
    ENSP00000404232.2, ENST00000420999.2
    Conserved Domains (2) summary
    smart00676
    Location:75 → 182
    DM10; Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases
    pfam06565
    Location:419 → 530
    DUF1126; DUF1126 PH-like domain

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    44147872..44343672 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047442535.1 → XP_047298491.1  EF-hand domain-containing family member C2 isoform X1

  2. XM_006724562.3 → XP_006724625.1  EF-hand domain-containing family member C2 isoform X3

    Conserved Domains (2) summary
    smart00676
    Location:236 → 342
    DM10; Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases
    pfam06565
    Location:258 → 290
    DUF1126; Repeat of unknown function (DUF1126)

  3. XM_047442536.1 → XP_047298492.1  EF-hand domain-containing family member C2 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    43554179..43750009 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327916.1 → XP_054183891.1  EF-hand domain-containing family member C2 isoform X1

  2. XM_054327918.1 → XP_054183893.1  EF-hand domain-containing family member C2 isoform X3

  3. XM_054327917.1 → XP_054183892.1  EF-hand domain-containing family member C2 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5JST6.2 GenPept UniProtKB/Swiss-Prot:Q5JST6

Gene LinkOut

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