PDE4DIP

phosphodiesterase 4D interacting protein

Basic information

Region (hg38): 1:148808139-149048286

Previous symbols: [ "CMYA2" ]

Links

ENSG00000178104 ∙ NCBI:9659 ∙ OMIM:608117 ∙ HGNC:15580 ∙ Uniprot:Q5VU43 ∙ 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 PDE4DIP gene.

• not provided (18 variants)
• See cases (4 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDE4DIP 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				14		14
missense	1	2	1		3	7
nonsense					1	1
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	1	2	1	14	5

Highest pathogenic variant AF is 0.00000657

Variants in PDE4DIP

This is a list of pathogenic ClinVar variants found in the PDE4DIP region.

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

Position	Type	Phenotype	Significance	ClinVar
1-148931908-C-G		Hepatocellular carcinoma	Pathogenic (Jun 15, 2021)
1-148953028-T-A			Benign (Sep 12, 2018)
1-148953102-A-C			not provided (-)
1-148953147-G-A		See cases	Pathogenic (Jun 01, 2021)
1-148953206-G-A			Likely benign (Feb 01, 2023)
1-148953402-A-G			Benign (May 04, 2018)
1-148953512-T-G			Likely benign (Apr 01, 2023)
1-148953659-C-T			Likely benign (Apr 01, 2023)
1-148960636-TTTGCCGTTTCTTCC-T			Benign (Sep 12, 2018)
1-148960744-GA-G		not specified	Benign (Mar 28, 2016)
1-148961952-G-A			Benign (Sep 12, 2018)
1-148962237-A-C			Likely benign (Mar 01, 2023)
1-148962551-C-T			Likely benign (May 04, 2018)
1-148962565-A-G			Likely benign (Apr 01, 2023)
1-148962598-C-T			Likely benign (Nov 01, 2022)
1-148962619-G-A			Likely benign (Mar 01, 2023)
1-148967799-G-A			Benign (Jan 17, 2024)
1-148968850-AC-A		Hepatocellular carcinoma	Pathogenic (Jun 15, 2021)
1-148968883-G-A			Likely benign (Nov 01, 2022)
1-148968914-C-T		Hepatocellular carcinoma	Pathogenic (Jun 15, 2021)
1-148991964-T-C			Likely benign (Mar 01, 2023)
1-149002894-G-A			Likely benign (Mar 01, 2023)
1-149002952-C-T		See cases	Likely pathogenic (Jun 01, 2021)
1-149003009-G-A			Likely benign (Feb 01, 2024)
1-149005085-C-T		Hepatocellular carcinoma	Pathogenic (Jun 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDE4DIP	protein_coding	protein_coding	ENST00000369356	44	240030

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.61e-37	0.907	121928	0	3820	125748	0.0153

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.40	1136	1.01e+3	1.12	0.0000525	14285
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00965	0.00965
Ashkenazi Jewish	0.0101	0.0102
East Asian	0.00152	0.00152
Finnish	0.0471	0.0478
European (Non-Finnish)	0.0164	0.0164
Middle Eastern	0.00152	0.00152
South Asian	0.0167	0.0166
Other	0.0103	0.0103

dbNSFP

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

Haploinsufficiency Scores

• ghis: 0.547

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pde4dip
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Gene ontology

• Biological process: cellular protein-containing complex assembly;regulation of Golgi organization
• Cellular component: nucleus;cytoplasm;Golgi apparatus;centrosome;myofibril
• Molecular function: protein binding;enzyme binding;protein-containing complex scaffold activity