MORC2
protein-codingMORC family CW-type zinc finger 2, the group of Zinc fingers CW-type
Gene summary
This gene encodes a member of the Microrchidia (MORC) protein superfamily. The encoded protein is known to regulate the condensation of heterochromatin in response to DNA damage and play a role in repressing transcription. The protein has been found to regulate the activity of ATP citrate lyase via specific interaction with this enzyme in the cytosol of lipogenic breast cancer cells. The protein also plays a role in lipogenesis and adipocyte differentiation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2016]
- ZCWCC1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~43.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0030835
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0014736
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0014736
Submitter: ClinGen
MORC2 was first reported in relation to Charcot-Marie-Tooth type 2Z (CMT2Z) in 2016 (Sevilla et al., PMID: 26497905; Albulym et al PMID: 26659848)). CMT2Z is allelic with ‘developmental delay, impaired growth, dysmorphic facies, and axonal neuropathy’ (DIGFAN). These diseases illustrate the diverse range of phenotypical expressions associated with MORC2, varying both in terms of age of onset and overall clinical presentation. Based on these extremely distinct disease presentations, we decided to split and curate the CMT2Z – MORC2 assertion. Patients with CMT2Z present with an axonal (sensori)motor peripheral neuropathy with varying inter- and intrafamilial severity. Complex features, such as central nervous system involvement, or more proximal weakness (non-5Q SMA presentation) are rarely reported (Jacquier et al., PMID 35904125). MORC2 encodes the Microrchidia (MORC) family CW-type zinc finger 2 protein, a DNA-dependent ATPase that plays a role in chromatin remodeling, DNA repair, and transcriptional regulation (Sancho et al., 2019, PMID: 30624633). Extensive genetic evidence is present to support the gene-disease relationship. In total, we scored evidence for 12 different missense variants in 27 probands, of which the mutation was found to be de novo in 9 probands. (Sevilla et al., PMID:26497905, Albulym et al., PMID: 26659848, Zhao et al., PMID: 27329773, Ando et al., PMID: 28771897, Duan et al., PMID: 34059105, Hyun et al., PMID: 27105897, Lassuthova et al., PMID: 26912637, Jacquier et al., PMID: 35904125, Sivera et al., PMID: 34189813, Vujovic et al., PMID: 33844363, Wang et al., PMID: 35332768). A summed LOD score of 9,72, calculated in three families, added substantially to the segregation evidence. Furthermore, experimental evidence supports the gene-disease relationship. The recurrent p.Arg252Trp mutation has been found to hyperactivate the HUSH complex, leading to a transcriptional repression of target genes. (Tchasovnikarova IA, et al., PMID: 28581500). These results were confirmed through transcriptome analysis in patient-derived fibroblasts (Sancho et al,PMID: 30624633). In summary, MORC2 is DEFINETIVELY associated with autosomal dominant axonal Charcot-Marie-Tooth disease. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time.
Inheritance Pattern: AD
Disease ID:MONDO:0009723
Submitter: ClinGen
The relationship between MORC2 and Leigh syndrome spectrum was evaluated using the ClinGen Clinical Validity Framework as of March 24, 2021. The MORC2 gene encodes Microrchidia family CW-type zinc finger 2, a DNA-dependent ATPase that has several important roles including in chromatin remodeling, DNA repair and regulating transcription. The MORC2 gene was first reported in relation to de novo dominant Leigh syndrome spectrum in 2019 (PMID: 30624633). Evidence supporting this gene-disease relationship includes case-level data and experimental data. This curation included two de novo variants identified in two cases in one publication (PMID: 30624633). No segregation data were available. MORC2 variants have also been reported to be associated with Charcot-Marie-Tooth disease type 2Z and a syndrome of developmental delay, impaired growth, dysmorphic facies, and axonal neuropathy (DIGFAN). Haploinsufficiency is implicated as the mechanism of disease but this is still being studied. This gene-disease association is also supported by expression (PMID: 25613900). In summary, there is limited evidence to support this gene-disease relationship. While more evidence is needed to establish this relationship definitively, no convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the NICHD U24 ClinGen Mitochondrial Disease Gene Curation Expert Panel on March 24, 2021 (SOP Version 7).
Inheritance Pattern: AD
Disease ID:MONDO:0030835
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0014736
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0014736
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Musculoskeletal; Neurologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MORC2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001303256.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 17 | 205 | 3 | 225 | ||
| missense | 9 | 34 | 454 | 38 | 535 | |
| nonsense | 15 | 15 | ||||
| start loss | 1 | 1 | ||||
| frameshift | 15 | 15 | ||||
| splice donor/acceptor (+/-2bp) | 13 | 13 | ||||
| Total | 9 | 34 | 515 | 243 | 3 | 804 |
Highest pathogenic variant AF is 6.8608375e-7
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001290185.1 | 26 | MANE Select | |
| Ensembl | ENSP00000380763.2 | 26 | MANE Select | |
| RefSeq | NP_001290186.1 | 26 | Standard | |
| RefSeq | NP_055756.1 | 23 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metabolism of lipids
- Fatty acyl-CoA biosynthesis
- Metabolism
- Fatty acid metabolism
Biological Process
- fatty acid metabolic process
Molecular Function
- zinc ion binding
Cellular Component
- nucleus
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000215862
- Coding exons
- 23
- Length
- 43168
- Individuals with no LoFs
- 125739
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 9
- Defined
- 125748
- p
- 0.0000358
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.23 | 376 | 598 | 0.629 | 0.0000374 | 6328 |
| Missense (PolyPhen) | 59 | 154.44 | 0.38203 | 1825 | ||
| Synonymous | 0.959 | 203 | 221 | 0.918 | 0.0000129 | 1903 |
| Loss of Function | 6.31 | 6 | 57.8 | 0.104 | 0.00000335 | 625 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0000089 | 0.0000088 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Exhibits a cytosolic function in lipogenesis, adipogenic differentiation, and lipid homeostasis by increasing the activity of ACLY, possibly preventing its dephosphorylation (PubMed:24286864). May act as a transcriptional repressor (PubMed:20225202). Down-regulates CA9 expression (PubMed:20110259). {ECO:0000269|PubMed:20110259, ECO:0000269|PubMed:20225202, ECO:0000269|PubMed:24286864}.;
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- RVIS EVS
- -1.68
- RVIS percentile EVS
- 2.63
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- E
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.977
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |