GeneBe

DYM

dymeclin, the group of Armadillo like helical domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 18:49036387-49461347

Links

ENSG00000141627 ∙ NCBI:54808 ∙ OMIM:607461 ∙ HGNC:21317 ∙ Uniprot:Q7RTS9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • Dyggve-Melchior-Clausen disease (Definitive), mode of inheritance: AR
  • Dyggve-Melchior-Clausen disease (Strong), mode of inheritance: AR
  • Smith-McCort dysplasia 1 (Moderate), mode of inheritance: AR
  • Dyggve-Melchior-Clausen disease (Supportive), mode of inheritance: AR
  • Smith-McCort dysplasia (Supportive), mode of inheritance: AR
  • Dyggve-Melchior-Clausen disease (Strong), mode of inheritance: AR
  • Smith-McCort dysplasia 1 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Dyggve-Melchior-Clausen disease; Smith-McCort dysplasia 1ARMusculoskeletalSpinal cord compression due to atlantoaxial instability has been described, and awareness may allow screening and management to avoid potential sequelaeMusculoskeletal; Neurologic21032395; 1008064; 401564; 679519; 2213845; 1486701; 12491225; 12554689; 16470731; 19005420; 20865280; 22090722

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DYM gene.

  • not_provided (237 variants)
  • Inborn_genetic_diseases (83 variants)
  • Dyggve-Melchior-Clausen_syndrome (65 variants)
  • Smith-McCort_dysplasia (23 variants)
  • DYM-related_disorder (19 variants)
  • Smith-McCort_dysplasia_1 (10 variants)
  • Connective_tissue_disorder (8 variants)
  • not_specified (4 variants)
  • Prostate_cancer (1 variants)
  • Schizophrenia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DYM gene is commonly pathogenic or not. These statistics are base on transcript: NM_001353214.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
5
clinvar
79
clinvar
1
clinvar
 85
missense
3
clinvar
1
clinvar
138
clinvar
7
clinvar
1
clinvar
 150
nonsense
9
clinvar
7
clinvar
 16
start loss
0
frameshift
13
clinvar
4
clinvar
 17
splice donor/acceptor (+/-2bp)
4
clinvar
10
clinvar
 14
Total 29 22 143 86 2

Highest pathogenic variant AF is 0.000023964034

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
DYMprotein_codingprotein_codingENST00000269445 16417679
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
3.59e-130.9011256770711257480.000282
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2393343470.9640.00001764365
Missense in Polyphen110130.510.842871705
Synonymous-0.4881441371.050.000007611281
Loss of Function2.032639.90.6520.00000226459

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0009480.000948
Ashkenazi Jewish0.000.00
East Asian0.0004900.000489
Finnish0.00004620.0000462
European (Non-Finnish)0.0002300.000229
Middle Eastern0.0004900.000489
South Asian0.0002620.000261
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Necessary for correct organization of Golgi apparatus. Involved in bone development. {ECO:0000269|PubMed:21280149}.;
Disease
DISEASE: Dyggve-Melchior-Clausen syndrome (DMC) [MIM:223800]: A rare autosomal recessive disorder belonging to the group of spondyloepimetaphyseal dysplasias. DMC is characterized by progressive short stature with short trunk dwarfism, microcephaly, protruding sternum, and psychomotor retardation. Radiological features include a platyspondyly with double vertebral humps, an epiphyso-metaphyseal dysplasia and lacy pelvis iliac crests. {ECO:0000269|PubMed:12491225, ECO:0000269|PubMed:12554689, ECO:0000269|PubMed:18996921}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Smith-McCort dysplasia 1 (SMC1) [MIM:607326]: A rare autosomal recessive osteochondrodysplasia with skeletal features identical to those of Dyggve-Melchior-Clausen syndrome, but with normal intelligence and no microcephaly. It is characterized by short limbs and trunk with barrel-shaped chest. The radiographic phenotype includes platyspondyly, generalized abnormalities of the epiphyses and metaphyses, and a distinctive lacy appearance of the iliac crest. {ECO:0000269|PubMed:12491225, ECO:0000269|PubMed:18996921, ECO:0000269|PubMed:19005420}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.164

Intolerance Scores

loftool
0.191
rvis_EVS
-0.75
rvis_percentile_EVS
13.67

Haploinsufficiency Scores

pHI
0.174
hipred
N
hipred_score
0.267
ghis
0.568

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.616

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Dym
Phenotype
limbs/digits/tail phenotype; renal/urinary system phenotype; skeleton phenotype; growth/size/body region phenotype; craniofacial phenotype; cellular phenotype;

Gene ontology

Biological process
Golgi organization;bone development
Cellular component
cytoplasm;Golgi apparatus;membrane
Molecular function
protein binding;enzyme binding