EFHD1 EF-hand domain family member D1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: EFHD1provided by HGNC
Official Full Name: EF-hand domain family member D1provided by HGNC
Primary source: HGNC:HGNC:29556
See related: Ensembl:ENSG00000115468 MIM:611617; AllianceGenome:HGNC:29556
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: SWS2; MST133; PP3051; MSTP133
Summary: This gene encodes a member of the EF-hand super family of calcium binding proteins, which are involved in a variety of cellular processes including mitosis, synaptic transmission, and cytoskeletal rearrangement. The protein encoded by this gene is composed of an N-terminal disordered region, proline-rich elements, two EF-hands, and a C-terminal coiled-coil domain. This protein has been shown to associate with the mitochondrial inner membrane, and in HeLa cells, acts as a novel mitochondrial calcium ion sensor for mitochondrial flash activation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]
Expression: Biased expression in kidney (RPKM 68.5), placenta (RPKM 36.8) and 12 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q37.1

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (232606057..232682776)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (233092814..233169537)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (233470767..233547486)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

EFHD1, a novel mitochondrial regulator of tumor metastasis in clear cell renal cell carcinoma.
Title: EFHD1, a novel mitochondrial regulator of tumor metastasis in clear cell renal cell carcinoma.
EFHD1 functions as a novel mitochondrial Ca(2+) sensor underlying Ca(2+)-dependent activation of mitoflashes
Title: Identification of EFHD1 as a novel Ca(2+) sensor for mitoflash activation.
detection of methylation of PPP1R3C alone or in combination with EFHD1 in plasma DNA showed high sensitivity and specificity in CRC detection, and may be useful detection method for CRC, especially for early-stage CRCs.
Title: Aberrant promoter methylation of PPP1R3C and EFHD1 in plasma of colorectal cancer patients.
Observational study of gene-disease association. (HuGE Navigator)
Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Cloning of novel mouse genes associated with neuronal function, including Efhd1.
Title: Novel genes cloned from a neuronal cell line newly established from a cerebellum of an adult p53(-/-) mouse.

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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

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

G20538 (e-PCR)
- UniSTS:81468

A005V33 (e-PCR)
- UniSTS:81469

RH45995 (e-PCR)
- UniSTS:16306

G31075 (e-PCR)
- UniSTS:57806

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion sensor activity	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion sensor activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in neuron projection development	IEA Inferred from Electronic Annotation more info
involved_in regulation of cellular hyperosmotic salinity response	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in mitochondrial inner membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in mitochondrion	TAS Traceable Author Statement more info	PubMed

General protein information

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Preferred Names: EF-hand domain-containing protein D1

Names: EF-hand domain-containing protein 1; swiprosin-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

NG_051251.1 RefSeqGene

Range

32548..81720

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001243252.2 → NP_001230181.1 EF-hand domain-containing protein D1 isoform 2

Status: REVIEWED

Description

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

Source sequence(s)

AK310565, BM677018, DB461847

Consensus CDS

CCDS58755.1

UniProtKB/TrEMBL

Q53SA2

Related

ENSP00000386556.1, ENST00000409613.5

Conserved Domains (1) summary

cd00051
Location:6 → 56

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 ...
NM_001308395.2 → NP_001295324.1 EF-hand domain-containing protein D1 isoform 3

See identical proteins and their annotated locations for NP_001295324.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains an alternate exon in its 5' UTR compared to variant 1. This variant represents translation initiation at a downstream start codon compared to variant 1; the 5'-most initiation codon, as used in variant 1, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the downstream start codon to encode an isoform (3) that has a significantly shorter N-terminus, compared to isoform 1.

Source sequence(s)

AK315442, BI460146, BU731354, CR627385, DB570289, DC328084

Consensus CDS

CCDS82580.1

UniProtKB/TrEMBL

Q53SA2, Q8WYH2

Related

ENSP00000386243.1, ENST00000409708.5

Conserved Domains (1) summary

cl08302
Location:2 → 40

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 ...
NM_025202.4 → NP_079478.1 EF-hand domain-containing protein D1 isoform 1

See identical proteins and their annotated locations for NP_079478.1

Status: REVIEWED

Description

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

Source sequence(s)

AC064852, AC073254, AF218006, BC002449

Consensus CDS

CCDS2497.1

UniProtKB/Swiss-Prot

B2RD83, E9PFH3, Q9BTF8, Q9BUP0, Q9H8I2, Q9HBQ0

UniProtKB/TrEMBL

Q59EU6

Related

ENSP00000264059.3, ENST00000264059.8

Conserved Domains (1) summary

cd00051
Location:94 → 152

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 ...