DMXL2 Dmx like 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: DMXL2provided by HGNC
Official Full Name: Dmx like 2provided by HGNC
Primary source: HGNC:HGNC:2938
See related: Ensembl:ENSG00000104093 MIM:612186; AllianceGenome:HGNC:2938
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: RC3; DEE81; PEPNS; DFNA71; EIEE81
Summary: This gene encodes a protein with 12 WD domains. Proteins with WD domains are involved in many functions including participation in signal transduction pathways. Participation of the encoded protein in regulation of the Notch signaling pathway has been demonstrated in vitro using several human cell lines (PMID:20810660). A gene encoding a similar protein is located on chromosome 5. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
Expression: Ubiquitous expression in brain (RPKM 8.0), bone marrow (RPKM 7.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q21.2

Exon count:: 47

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (51447791..51622771, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (49255566..49430224, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (51739988..51914968, complement)

Chromosome 15 - NC_000015.10 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
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?

A novel variant in DMXL2 gene is associated with autosomal dominant non-syndromic hearing impairment (DFNA71) in a Cameroonian family.
Title: A novel variant in DMXL2 gene is associated with autosomal dominant non-syndromic hearing impairment (DFNA71) in a Cameroonian family.
Disruption of DMXL2 may predispose to NDDs including autism spectrum disorder.
Title: Rare copy number variations affecting the synaptic gene DMXL2 in neurodevelopmental disorders.
Impaired lysosomal function and autophagy caused by biallelic DMXL2 mutations affect neuronal development and synapse formation and result in Ohtahara syndrome with profound developmental impairment and reduced life expectancy.
Title: Biallelic DMXL2 mutations impair autophagy and cause Ohtahara syndrome with progressive course.
Data indicated that the p.Arg2417His variant in DMXL2 is associated with dominant, nonsyndromic hearing loss and suggested an important role of DMXL2 in inner ear function.
Title: A dominant variant in DMXL2 is linked to nonsyndromic hearing loss.
authors demonstrate that DMXL2 is a transmembrane protein with a potential extra-cellular domain. These findings identify DMXL2 as a novel, functional biomarker for ERalpha positive breast cancer.
Title: DMXL2 drives epithelial to mesenchymal transition in hormonal therapy resistant breast cancer through Notch hyper-activation.
Haploinsufficiency of Dmxl2, encoding a synaptic protein, causes infertility associated with a loss of GnRH neurons in humans and mice.
Title: Haploinsufficiency of Dmxl2, encoding a synaptic protein, causes infertility associated with a loss of GnRH neurons in mouse.
an important role for Rabconnectin-3 and V-ATPase activity in the Notch signaling pathway in mammalian cells.
Title: Rabconnectin-3 is a functional regulator of mammalian Notch signaling.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene variants associated with ischemic stroke: the cardiovascular health study.

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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

Associated conditions

Description	Tests
Developmental and epileptic encephalopathy, 81 MedGen: C5231450 OMIM: 618663 GeneReviews: Not available	not available
Hearing loss, autosomal dominant 71 MedGen: C4539881 OMIM: 617605 GeneReviews: Not available	not available
Polyendocrine-polyneuropathy syndrome MedGen: C4015261 OMIM: 616113 GeneReviews: Not available	not available

Copy number response

Description
Copy number response Haploinsufficency No evidence available (Last evaluated 2012-04-04) ClinGen Genome Curation Page Triplosensitivity No evidence available (Last evaluated 2012-04-04) ClinGen Genome Curation Page

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

SHGC-32630 (e-PCR)
- UniSTS:22818

RH104279 (e-PCR)
- UniSTS:98604

RC3__5662 (e-PCR)
- UniSTS:468644

G20445 (e-PCR)
- UniSTS:43233

A005R29 (e-PCR)
- UniSTS:43234

D11S3316 (e-PCR)
- UniSTS:152558

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables small GTPase binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in vacuolar acidification	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of RAVE complex	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	HDA more info	PubMed
located_in neuronal dense core vesicle	IEA Inferred from Electronic Annotation more info
located_in synaptic vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: dmX-like protein 2

Names: rabconnectin-3

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_017155.1 RefSeqGene

Range

5000..179980

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001174116.3 → NP_001167587.1 dmX-like protein 2 isoform 1

Status: REVIEWED

Description

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

Source sequence(s)

AC020892, AC066613

Consensus CDS

CCDS53946.1

UniProtKB/Swiss-Prot

Q8TDJ6

Related

ENSP00000441858.2, ENST00000543779.6

Conserved Domains (4) summary

COG2319
Location:2778 → 2984

WD40; WD40 repeat [General function prediction only]

pfam12234
Location:1171 → 1902

Rav1p_C; RAVE protein 1 C terminal

sd00039
Location:2811 → 2851

7WD40; WD40 repeat [structural motif]

cl02567
Location:2767 → 3019

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001174117.3 → NP_001167588.1 dmX-like protein 2 isoform 3

See identical proteins and their annotated locations for NP_001167588.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks two coding exons compared to variant 1. The resulting protein (isoform 3) is shorter but has the same N- and C- termini compared to isoform 1.

Source sequence(s)

AC020892, AC066613

Consensus CDS

CCDS53945.1

UniProtKB/Swiss-Prot

Q8TDJ6

Related

ENSP00000400855.3, ENST00000449909.7

Conserved Domains (4) summary

COG2319
Location:2135 → 2347

WD40; WD40 repeat [General function prediction only]

pfam12234
Location:923 → 1266

Rav1p_C; RAVE protein 1 C terminal

sd00039
Location:2174 → 2214

7WD40; WD40 repeat [structural motif]

cl02567
Location:2130 → 2382

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001378457.1 → NP_001365386.1 dmX-like protein 2 isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) represents the longest transcript and encodes the longest isoform (4).

Source sequence(s)

AC020892, AC066613

Consensus CDS

CCDS91998.1

UniProtKB/TrEMBL

H0YLM8

Related

ENSP00000453267.2, ENST00000560891.6

Conserved Domains (3) summary

sd00039
Location:2832 → 2872

7WD40; WD40 repeat [structural motif]

pfam12234
Location:1171 → 1902

Rav1p_C; RAVE protein 1 C terminal

cl29593
Location:2788 → 3040

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001378458.1 → NP_001365387.1 dmX-like protein 2 isoform 5

Status: REVIEWED

Source sequence(s)

AC020892, AC066613

Conserved Domains (3) summary

sd00039
Location:2831 → 2871

7WD40; WD40 repeat [structural motif]

pfam12234
Location:1171 → 1902

Rav1p_C; RAVE protein 1 C terminal

cl29593
Location:2787 → 3039

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001378459.1 → NP_001365388.1 dmX-like protein 2 isoform 6

Status: REVIEWED

Source sequence(s)

AC020892, AC066613

Conserved Domains (3) summary

sd00039
Location:2736 → 2776

7WD40; WD40 repeat [structural motif]

pfam12234
Location:1171 → 1902

Rav1p_C; RAVE protein 1 C terminal

cl29593
Location:2692 → 2944

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001378460.1 → NP_001365389.1 dmX-like protein 2 isoform 7

Status: REVIEWED

Source sequence(s)

AC020892, AC066613

Conserved Domains (3) summary

sd00039
Location:2137 → 2177

7WD40; WD40 repeat [structural motif]

pfam12234
Location:909 → 1229

Rav1p_C; RAVE protein 1 C terminal

cl29593
Location:2093 → 2345

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001378461.1 → NP_001365390.1 dmX-like protein 2 isoform 8

Status: REVIEWED

Source sequence(s)

AC020892, AC066613

Conserved Domains (2) summary

sd00039
Location:61 → 102

7WD40; WD40 repeat [structural motif]

pfam12234
Location:1171 → 1902

Rav1p_C; RAVE protein 1 C terminal
NM_001378462.1 → NP_001365391.1 dmX-like protein 2 isoform 9

Status: REVIEWED

Source sequence(s)

AC020892, AC066613

Conserved Domains (2) summary

sd00039
Location:61 → 102

7WD40; WD40 repeat [structural motif]

pfam12234
Location:1171 → 1902

Rav1p_C; RAVE protein 1 C terminal
NM_001378463.1 → NP_001365392.1 dmX-like protein 2 isoform 10

Status: REVIEWED

Source sequence(s)

AC020892, AC066613

Conserved Domains (2) summary

sd00039
Location:61 → 102

7WD40; WD40 repeat [structural motif]

pfam12234
Location:1171 → 1902

Rav1p_C; RAVE protein 1 C terminal
NM_001378464.1 → NP_001365393.1 dmX-like protein 2 isoform 11

Status: REVIEWED

Source sequence(s)

AC020892, AC066613

Conserved Domains (2) summary

sd00039
Location:61 → 102

7WD40; WD40 repeat [structural motif]

pfam12234
Location:1091 → 1822

Rav1p_C; RAVE protein 1 C terminal
NM_015263.5 → NP_056078.2 dmX-like protein 2 isoform 2

See identical proteins and their annotated locations for NP_056078.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.

Source sequence(s)

AC020892, AC066613

Consensus CDS

CCDS10141.1

UniProtKB/Swiss-Prot

B2RTR3, B7ZMH3, F5GWF1, O94938, Q8TDJ6

Related

ENSP00000251076.5, ENST00000251076.9

Conserved Domains (4) summary

COG2319
Location:2777 → 2983

WD40; WD40 repeat [General function prediction only]

pfam12234
Location:1171 → 1902

Rav1p_C; RAVE protein 1 C terminal

sd00039
Location:2810 → 2850

7WD40; WD40 repeat [structural motif]

cl02567
Location:2766 → 3018

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RNA

NR_165648.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC020892, AC066613
NR_165649.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC020892, AC066613