1-149003009-G-C

Variant names:

• chr1-149003009-G-C
• rs147815016
• NM_001395426.1:c.3931G>C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001395426.1(PDE4DIP):​c.3931G>C​(p.Ala1311Pro) variant causes a missense change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A1311T) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 20)
• Consequence: PDE4DIP NM_001395426.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.46

Genes affected

PDE4DIP (HGNC:15580): (phosphodiesterase 4D interacting protein) 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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDE4DIP	NM_001395426.1	c.3931G>C	p.Ala1311Pro	missense_variant	Exon 28 of 47	ENST00000695795.1	NP_001382355.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDE4DIP	ENST00000695795.1	c.3931G>C	p.Ala1311Pro	missense_variant	Exon 28 of 47		NM_001395426.1	ENSP00000512175.1

Frequencies

GnomAD3 genomes Cov.: 20

GnomAD4 exome Cov.: 6

GnomAD4 genome Cov.: 20

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.94
BayesDel_noAF	Pathogenic	0.31
CADD	Pathogenic	28
DANN	Uncertain	1.0
DEOGEN2	Benign	0.033	.;T;.;.;T
LIST_S2	Uncertain	0.90	D;D;D;D;D
MetaRNN	Uncertain	0.60	D;D;D;D;D
PROVEAN	Uncertain	-3.0	.;.;.;D;D
Sift	Benign	0.038	.;.;.;D;D
Sift4G	Uncertain	0.0080	D;D;D;D;D
Vest4		0.70
gMVP		0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs147815016; hg19: chr1-144881463;