EFHC1 EF-hand domain containing 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: EFHC1provided by HGNC
Official Full Name: EF-hand domain containing 1provided by HGNC
Primary source: HGNC:HGNC:16406
See related: Ensembl:ENSG00000096093 MIM:608815; AllianceGenome:HGNC:16406
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: EJM1; POC9; RIB72; dJ304B14.2
Summary: This gene encodes an EF-hand-containing calcium binding protein. The encoded protein likely plays a role in calcium homeostasis. Mutations in this gene have been associated with susceptibility to juvenile myoclonic epilepsy and juvenile absence epilepsy. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2010]
Expression: Broad expression in testis (RPKM 8.2), thyroid (RPKM 5.9) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p12.2

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (52420342..52497198)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (52259137..52336010)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (52285140..52361996)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

EFHC1 gene mutation profile of Turkish JME patients and its association with disease risk.
Title: EFHC1 gene mutation profile of Turkish JME patients and its association with disease risk.
Mutational Analysis of Myoclonin1 Gene in Pakistani Juvenile Myoclonic Epilepsy Patients.
Title: Mutational Analysis of Myoclonin1 Gene in Pakistani Juvenile Myoclonic Epilepsy Patients.
Revisiting the clinical impact of variants in EFHC1 in patients with different phenotypes of genetic generalized epilepsy.
Title: Revisiting the clinical impact of variants in EFHC1 in patients with different phenotypes of genetic generalized epilepsy.
EFHC1 mutations cause microtubule-associated defects in juvenile myoclonic epilepsy
Title: Microtubule-associated defects caused by EFHC1 mutations in juvenile myoclonic epilepsy.
NHGRI gene-level evidence and variant-level evidence establish EFHC1 as the first non-ion channel microtubule-associated protein whose mutations disturb R-type VDCC and TRPM2 calcium currents in overgrown synapses and dendrites within abnormally migrated dislocated neurons, thus explaining CTC convulsions and "microdysgenesis" neuropathology of juvenile myoclonic epilepsy
Title: EFHC1 variants in juvenile myoclonic epilepsy: reanalysis according to NHGRI and ACMG guidelines for assigning disease causality.
some EFHC1 mutations may be pathogenic only when introduced into specific genetic backgrounds to juvenile myoclonic epilepsy
Title: Pathogenic EFHC1 mutations are tolerated in healthy individuals dependent on reported ancestry.
Three SNP alleles in BRD2, Cx-36, and ME2 and microdeletions in 15q13.3, 15q11.2, and 16p13.11 also contribute risk to juvenile myclonic epilepsy.
Title: Juvenile myoclonic epilepsy as a possible neurodevelopmental disease: role of EFHC1 or Myoclonin1.
Myoclonin1/EFHC1 mutation was suggested releated to juvenile myoclonic epilepsy.
Title: The quest for juvenile myoclonic epilepsy genes.
These results show how Myoclonin1/EFHC1 mutations disrupt brain development and potentially produce structural brain abnormalities on which epileptogenesis is established.
Title: Mutations of EFHC1, linked to juvenile myoclonic epilepsy, disrupt radial and tangential migrations during brain development.
we conclude that mutations in the Myoclonin1/EFHC1 gene are an important cause of juvenile myoclonic epilepsy in Mexican patients.
Title: Novel Myoclonin1/EFHC1 mutations in Mexican patients with juvenile myoclonic epilepsy.

Submit: New GeneRIF Correction See all GeneRIFs (26)

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
Epilepsy, juvenile absence, susceptibility to, 1 MedGen: C2750892 OMIM: 607631 GeneReviews: Not available	Compare labs
Myoclonic epilepsy, juvenile, susceptibility to, 1 MedGen: C1850778 OMIM: 254770 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-AA037246 (e-PCR)
- UniSTS:3605

RH102236 (e-PCR)
- UniSTS:96570

NIB1406 (e-PCR)
- UniSTS:56676

D1S1423 (e-PCR)
- UniSTS:149619

SHGC-81734 (e-PCR)
- UniSTS:103906

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables alpha-tubulin binding	IBA Inferred from Biological aspect of Ancestor more info
enables alpha-tubulin binding	IDA Inferred from Direct Assay more info	PubMed
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in cerebral cortex cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cilium-dependent cell motility	IBA Inferred from Biological aspect of Ancestor more info
involved_in flagellated sperm motility	ISS Inferred from Sequence or Structural Similarity more info
involved_in mitotic cytokinesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitotic cytokinesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitotic spindle organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitotic spindle organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cell division	IMP Inferred from Mutant Phenotype more info	PubMed

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
is_active_in axoneme	IBA Inferred from Biological aspect of Ancestor more info
located_in axoneme	ISS Inferred from Sequence or Structural Similarity more info
located_in centrosome	IDA Inferred from Direct Assay more info	PubMed
is_active_in mitotic spindle	IBA Inferred from Biological aspect of Ancestor more info
located_in mitotic spindle	IDA Inferred from Direct Assay more info	PubMed
located_in neuronal cell body	ISS Inferred from Sequence or Structural Similarity more info
is_active_in sperm flagellum	ISS Inferred from Sequence or Structural Similarity more info
located_in spindle pole	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: EF-hand domain-containing protein 1

Names: EF-hand domain (C-terminal) containing 1; myoclonin-1

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

NG_016760.1 RefSeqGene

Range

5147..82003

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001172420.2 → NP_001165891.1 EF-hand domain-containing protein 1 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (C) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant A. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AK297632, AL049611, AY608689, BQ268404, EU520261

Consensus CDS

CCDS55021.1

UniProtKB/TrEMBL

A0A1B0GTB1

Related

ENSP00000489966.1, ENST00000636954.1

Conserved Domains (4) summary

smart00676
Location:74 → 179

DM10; Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases

cd00051
Location:560 → 620

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

pfam06565
Location:103 → 134

DUF1126; Repeat of unknown function (DUF1126)

pfam13499
Location:560 → 619

EF-hand_7; EF-hand domain pair
NM_018100.4 → NP_060570.2 EF-hand domain-containing protein 1 isoform 1

See identical proteins and their annotated locations for NP_060570.2

Status: REVIEWED

Description

Transcript Variant: This variant (A) encodes the longer isoform (1).

Source sequence(s)

AK001328, AL049611, BC020210, BQ270560

Consensus CDS

CCDS4942.1

UniProtKB/Swiss-Prot

B4DMU3, F5GZD8, Q5JVL4, Q5XKM4, Q6E1U7, Q6E1U8, Q8WUL2, Q9NVW6

UniProtKB/TrEMBL

A0A1B0GTB1, B2CKC5

Related

ENSP00000360107.4, ENST00000371068.11

Conserved Domains (4) summary

smart00676
Location:93 → 198

DM10; Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases

cd00051
Location:579 → 639

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

pfam06565
Location:122 → 153

DUF1126; Repeat of unknown function (DUF1126)

pfam13499
Location:579 → 638

EF-hand_7; EF-hand domain pair

RNA

NR_033327.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (B) contains an alternate segment, compared to variant A. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant A, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK001328, AK225543, AL049611, AL122084, BQ268404