PDE4DIP

protein-coding

phosphodiesterase 4D interacting protein

Gene summary

The protein encoded by this gene serves to anchor phosphodiesterase 4D to the Golgi/centrosome region of the cell. Defects in this gene may be a cause of myeloproliferative disorder (MBD) associated with eosinophilia. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2010]

Previous symbols:

CMYA2

MANE transcript

NM_001395426.1

Inheritance

—

ClinVar variants

P:2U:53B:19

Top phenotype

See cases

gnomAD constraint

pLI —, LoF o/e 0.68

Max pathogenic AF

—

Genomic locus

chr1:148,808,140-149,048,286

External References & Databases

Ensembl (ENSG00000178104)

Transcript & Mutation Effects

hg38 • Region Span ~240.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PDE4DIP variants in ClinVar

3 Conditions Cataloged

not providedTotal: 22

not specifiedTotal: 6

See casesTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001395426.1. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	11 clinvar		14
missense		2 clinvar	25 clinvar	5 clinvar	1 clinvar	33
nonsense			8 clinvar		1 clinvar	9
start loss						0
frameshift			6 clinvar		1 clinvar	7
splice donor/acceptor (+/-2bp)			11 clinvar			11
Total	0	2	53	16	3	74

Highest pathogenic variant AF is 0.00019137713

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 106 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001395426.1	RefSeq	NP_001382355.1	47	MANE Select
ENST00000695795.1	Ensembl	ENSP00000512175.1	47	MANE Select
NM_001002810.5	RefSeq	NP_001002810.1	4	Standard
NM_001002811.3	RefSeq	NP_001002811.2	19	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cellular protein-containing complex assembly
regulation of Golgi organization

Molecular Function

protein binding
enzyme binding
protein-containing complex scaffold activity

Cellular Component

nucleus
cytoplasm
Golgi apparatus
centrosome
myofibril

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369356
Coding exons: 44
Length: 240030
Individuals with no LoFs: 121928
Homozygous LoFs: 0
Heterozygous LoFs: 3820
Defined: 125748
p: 0.0153

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.40	1136	1.01e+3	1.12	0.0000525	14285
Missense (PolyPhen)		365	366.66	0.99547		5461
Synonymous	0.266	376	383	0.983	0.0000186	4083
Loss of Function	3.13	76	112	0.680	0.00000603	1376

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0039	0.0039	notable
Latino/Admixed American	0.0057	0.0057	notable
Ashkenazi Jewish	0.010	0.010	notable
East Asian	0.0015	0.0015	notable
Finnish	0.047	0.048	notable
European (Non-Finnish)	0.016	0.016	notable
South Asian	0.017	0.017	notable
Other	0.010	0.010	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Functions as an anchor sequestering components of the cAMP-dependent pathway to Golgi and/or centrosomes (By similarity). {ECO:0000250|UniProtKB:Q9WUJ3}.;
Disease: DISEASE: Note=A chromosomal aberration involving PDE4DIP may be the cause of a myeloproliferative disorder (MBD) associated with eosinophilia. Translocation t(1;5)(q23;q33) that forms a PDE4DIP- PDGFRB fusion protein. {ECO:0000269|PubMed:12907457}.;

Intolerance Scores

LoFtool: 0.984
RVIS EVS: 7.99
RVIS percentile EVS: 99.95

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 1.00

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High