DPCD

deleted in primary ciliary dyskinesia homolog (mouse), the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 10:101570559-101609662

Links

ENSG00000166171 ∙ NCBI:25911 ∙ OMIM:616467 ∙ HGNC:24542 ∙ Uniprot:Q9BVM2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (8 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPCD 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						0
missense			8		1	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	1

Variants in DPCD

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

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

Position	Type	Phenotype	Significance	ClinVar
10-101579385-G-A			Benign (May 15, 2021)
10-101579569-G-A		not specified	Uncertain significance (Nov 08, 2022)
10-101579577-G-A		not specified	Uncertain significance (Nov 21, 2022)
10-101579635-T-C		not specified	Uncertain significance (Jul 14, 2021)
10-101579641-G-A		not specified	Uncertain significance (Feb 27, 2024)
10-101579649-T-C		not specified	Uncertain significance (Jan 04, 2024)
10-101579671-G-A		not specified	Uncertain significance (May 06, 2022)
10-101579690-G-T		POLL-related disorder	Likely benign (Feb 10, 2022)
10-101579710-T-C		POLL-related disorder	Likely benign (Jul 30, 2023)
10-101579721-C-T		not specified	Uncertain significance (Aug 12, 2021)
10-101579728-G-A		not specified	Uncertain significance (Oct 12, 2022)
10-101579731-G-A		not specified	Likely benign (May 11, 2022)
10-101579749-G-A		not specified	Uncertain significance (Feb 06, 2024)
10-101579770-G-C		not specified	Uncertain significance (Dec 05, 2022)
10-101579778-C-T		not specified	Uncertain significance (May 23, 2023)
10-101580253-T-C		not specified	Uncertain significance (Jan 09, 2024)
10-101580257-G-A		not specified	Uncertain significance (Oct 27, 2023)
10-101580286-C-G		not specified	Uncertain significance (Nov 09, 2021)
10-101580290-G-A		not specified	Uncertain significance (Aug 17, 2021)
10-101580299-G-A			Benign (May 04, 2021)
10-101580302-C-T		not specified	Uncertain significance (Nov 05, 2021)
10-101580324-G-A			Likely benign (Feb 01, 2024)
10-101580326-C-T		not specified	Uncertain significance (Jul 20, 2021)
10-101580374-C-T		not specified	Uncertain significance (Jan 26, 2022)
10-101580387-A-G			Benign (May 04, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPCD	protein_coding	protein_coding	ENST00000370151	6	39109

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000288	0.808	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.279	108	116	0.927	0.00000627	1331
Missense in Polyphen		27	42.59	0.63396		462
Synonymous	0.837	38	45.2	0.841	0.00000272	372
Loss of Function	1.16	7	11.2	0.626	5.37e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000231	0.000231
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000981	0.0000967
Middle Eastern	0.000165	0.000163
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the formation or function of ciliated cells. {ECO:0000269|PubMed:14630615}.

Intolerance Scores

• loftool: 0.762
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.18

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.562
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dpcd
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system 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); reproductive system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; immune system phenotype; skeleton phenotype; growth/size/body region phenotype; craniofacial phenotype; cellular phenotype

Gene ontology

• Biological process: epithelial cilium movement;spermatogenesis;determination of left/right symmetry;lateral ventricle development;third ventricle development;flagellated sperm motility;left/right pattern formation
• Cellular component: nucleus
• Molecular function: protein binding