DCPS

decapping enzyme, scavenger, the group of Histidine triad superfamily

Basic information

Region (hg38): 11:126304059-126350005

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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Al-Raqad syndrome	AR	General	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	Craniofacial; Musculoskeletal; Neurologic	25701870; 25712129

ClinVar

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

• not provided (29 variants)
• Inborn genetic diseases (20 variants)
• Al-Raqad syndrome (13 variants)
• not specified (4 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				12	4	16
missense		2	27	5		34
nonsense		2				2
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	1		2
non coding				1		1
Total	0	4	28	18	4

Highest pathogenic variant AF is 0.000144

Variants in DCPS

This is a list of pathogenic ClinVar variants found in the DCPS region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-126304097-C-T		Inborn genetic diseases	Uncertain significance (Mar 24, 2023)
11-126304105-G-C		Inborn genetic diseases	Uncertain significance (Aug 09, 2021)
11-126304117-C-A		Inborn genetic diseases	Uncertain significance (Jan 02, 2024)
11-126304121-A-G		Inborn genetic diseases	Uncertain significance (Dec 16, 2022)
11-126304143-C-T			Benign (Nov 16, 2020)
11-126304151-G-A		Inborn genetic diseases	Uncertain significance (Jun 13, 2023)
11-126304167-G-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Sep 13, 2021)
11-126304216-G-A		Inborn genetic diseases	Uncertain significance (Nov 08, 2022)
11-126304241-G-T		Inborn genetic diseases	Uncertain significance (Jan 31, 2023)
11-126304269-C-T		Al-Raqad syndrome	Benign (Jul 30, 2021)
11-126304282-G-T		Al-Raqad syndrome	Likely pathogenic (Sep 27, 2023)
11-126304283-T-C		Al-Raqad syndrome	Pathogenic (Jul 29, 2019)
11-126304285-C-G		Al-Raqad syndrome	Uncertain significance (Jan 17, 2019)
11-126306583-C-CTGGGGA		Al-Raqad syndrome	Benign (May 04, 2023)
11-126306595-A-T		Inborn genetic diseases	Uncertain significance (Aug 22, 2023)
11-126306608-C-T			Likely benign (Sep 01, 2023)
11-126306628-C-T		Al-Raqad syndrome	Pathogenic (Jul 29, 2019)
11-126306641-G-A			Likely benign (Nov 15, 2017)
11-126306651-G-C		Inborn genetic diseases	Uncertain significance (Mar 30, 2022)
11-126306683-G-A		Al-Raqad syndrome	Benign (Jul 30, 2021)
11-126306697-A-G		Al-Raqad syndrome	Uncertain significance (May 19, 2020)
11-126330381-C-T			Likely benign (Jan 01, 2024)
11-126331414-C-T		Al-Raqad syndrome	Uncertain significance (May 19, 2020)
11-126331443-C-T		Inborn genetic diseases	Uncertain significance (Jan 30, 2024)
11-126331461-C-T		Inborn genetic diseases	Uncertain significance (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCPS	protein_coding	protein_coding	ENST00000263579	6	41998

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.47e-7	0.497	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.495	228	208	1.10	0.0000126	2188
Missense in Polyphen		55	54.582	1.0077		554
Synonymous	-0.997	104	91.8	1.13	0.00000576	684
Loss of Function	0.855	12	15.7	0.767	8.35e-7	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000362	0.000362
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000972	0.0000967
Middle Eastern	0.000109	0.000109
South Asian	0.0000328	0.0000327
Other	0.000164	0.000163

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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