MORC2

protein-coding

MORC 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]

Previous symbols:
  • ZCWCC1

MANE transcript

NM_001303256.3

Inheritance

AD

ClinVar variants

P:43U:515B:246

Top phenotype

Charcot-Marie-Tooth disease type, axonal, type 2Z; Developmental delay, impaired growth, dysmorphic facies, and axonal neuropathy

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr22:30,925,130-30,968,774

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~43.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

developmental delay, impaired growth, dysmorphic facies, and axonal neuropathySTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0030835

Submitter: G2P

Charcot-Marie-Tooth disease axonal type 2ZSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014736

Submitter: Labcorp Genetics (formerly Invitae)

Charcot-Marie-Tooth disease axonal type 2ZDEFINITIVE

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.

Leigh syndromeLIMITED

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).

developmental delay, impaired growth, dysmorphic facies, and axonal neuropathySTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0030835

Submitter: Labcorp Genetics (formerly Invitae)

Charcot-Marie-Tooth disease axonal type 2ZSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0014736

Submitter: Orphanet

Charcot-Marie-Tooth disease axonal type 2ZSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014736

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Charcot-Marie-Tooth disease type, axonal, type 2Z; Developmental delay, impaired growth, dysmorphic facies, and axonal neuropathyAD

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

Refs: 26497905; 27105897; 28771897; 32693025Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MORC2 variants in ClinVar

17 Conditions Cataloged
Charcot-Marie-Tooth disease axonal type 2ZTotal: 848
not providedTotal: 251
MORC2-related disorderTotal: 90
not specifiedTotal: 89
Inborn genetic diseasesTotal: 68
Developmental delay, impaired growth, dysmorphic facies, and axonal neuropathyTotal: 66
Charcot-Marie-Tooth diseaseTotal: 9
Neurodevelopmental disorderTotal: 2

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.

EffectPLPVUSLBBSum
synonymous
17
clinvar
205
clinvar
3
clinvar
225
missense
9
clinvar
34
clinvar
454
clinvar
38
clinvar
535
nonsense
15
clinvar
15
start loss
1
clinvar
1
frameshift
15
clinvar
15
splice donor/acceptor (+/-2bp)
13
clinvar
13
Total9345152433804

Highest pathogenic variant AF is 6.8608375e-7

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001303256.3RefSeqNP_001290185.126MANE Select
ENST00000397641.8EnsemblENSP00000380763.226MANE Select
NM_001303257.2RefSeqNP_001290186.126Standard
NM_014941.3RefSeqNP_055756.123Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.233765980.6290.00003746328
Missense (PolyPhen)59154.440.382031825
Synonymous0.9592032210.9180.00001291903
Loss of Function6.31657.80.1040.00000335625

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000870.000087rare
Ashkenazi Jewish00.0absent
East Asian0.000110.00011rare
Finnish00.0absent
European (Non-Finnish)0.00000890.0000088rare
South Asian0.0000980.000098rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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