GeneBe

DCPS

decapping enzyme, scavenger, the group of Histidine triad superfamily

Basic information

Region (hg38): 11:126304060-126350005

Links

ENSG00000110063 ∙ NCBI:28960 ∙ OMIM:610534 ∙ HGNC:29812 ∙ Uniprot:Q96C86 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • Al-Raqad syndrome (Moderate), mode of inheritance: AR
  • Al-Raqad syndrome (Strong), mode of inheritance: AR
  • autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Al-Raqad syndromeARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Musculoskeletal; Neurologic25701870; 25712129

ClinVar

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

  • Inborn_genetic_diseases (54 variants)
  • not_provided (32 variants)
  • Al-Raqad_syndrome (18 variants)
  • not_specified (7 variants)
  • DCPS-related_disorder (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCPS gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014026.6. 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
12
clinvar
1
clinvar
 13
missense
1
clinvar
2
clinvar
65
clinvar
8
clinvar
 76
nonsense
2
clinvar
 2
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
2
clinvar
1
clinvar
2
clinvar
 5
Total 3 5 68 20 1

Highest pathogenic variant AF is 0.000550814

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
DCPSprotein_codingprotein_codingENST00000263579 641998
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
2.47e-70.4971257240241257480.0000954
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.4952282081.100.00001262188
Missense in Polyphen5554.5821.0077554
Synonymous-0.99710491.81.130.00000576684
Loss of Function0.8551215.70.7678.35e-7170

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003620.000362
Ashkenazi Jewish0.00009920.0000992
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.00009720.0000967
Middle Eastern0.0001090.000109
South Asian0.00003280.0000327
Other0.0001640.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Decapping scavenger enzyme that catalyzes the cleavage of a residual cap structure following the degradation of mRNAs by the 3'->5' exosome-mediated mRNA decay pathway. Hydrolyzes cap analog structures like 7-methylguanosine nucleoside triphosphate (m7GpppG) with up to 10 nucleotide substrates (small capped oligoribonucleotides) and specifically releases 5'-phosphorylated RNA fragments and 7-methylguanosine monophosphate (m7GMP). Cleaves cap analog structures like tri-methyl guanosine nucleoside triphosphate (m3(2,2,7)GpppG) with very poor efficiency. Does not hydrolyze unmethylated cap analog (GpppG) and shows no decapping activity on intact m7GpppG-capped mRNA molecules longer than 25 nucleotides. Does not hydrolyze 7-methylguanosine diphosphate (m7GDP) to m7GMP (PubMed:22985415). May also play a role in the 5'->3 mRNA decay pathway; m7GDP, the downstream product released by the 5'->3' mRNA mediated decapping activity, may be also converted by DCPS to m7GMP (PubMed:14523240). Binds to m7GpppG and strongly to m7GDP. Plays a role in first intron splicing of pre- mRNAs. Inhibits activation-induced cell death. {ECO:0000269|PubMed:11747811, ECO:0000269|PubMed:12198172, ECO:0000269|PubMed:12871939, ECO:0000269|PubMed:14523240, ECO:0000269|PubMed:15273322, ECO:0000269|PubMed:15383679, ECO:0000269|PubMed:15769464, ECO:0000269|PubMed:16140270, ECO:0000269|PubMed:18426921, ECO:0000269|PubMed:22985415}.;
Disease
DISEASE: Al-Raqad syndrome (ARS) [MIM:616459]: A syndrome characterized by delayed psychomotor development, moderate to severe intellectual disability, poor or absent speech, microcephaly, congenital hypotonia, and severe growth delay. {ECO:0000269|PubMed:25701870, ECO:0000269|PubMed:25712129}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
RNA degradation - Homo sapiens (human);Metabolism of RNA;mRNA decay by 3, to 5, exoribonuclease;Deadenylation-dependent mRNA decay (Consensus)

Recessive Scores

pRec
0.192

Intolerance Scores

loftool
0.322
rvis_EVS
-0.18
rvis_percentile_EVS
40.56

Haploinsufficiency Scores

pHI
0.241
hipred
N
hipred_score
0.170
ghis
0.593

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.521

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Dcps
Phenotype
mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; growth/size/body region phenotype;

Gene ontology

Biological process
nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay;deadenylation-dependent decapping of nuclear-transcribed mRNA;cellular response to menadione;negative regulation of programmed cell death;exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay;mRNA cis splicing, via spliceosome;RNA phosphodiester bond hydrolysis, exonucleolytic
Cellular component
P-body;nucleus;nucleoplasm;cytoplasm;mitochondrion;cytosol
Molecular function
RNA 7-methylguanosine cap binding;exoribonuclease activity;protein binding;m7G(5')pppN diphosphatase activity