NM_001104631.2(PDE4D):c.682C>G (p.Gln228Glu) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 3, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003556069.1

Allele description [Variation Report for NM_001104631.2(PDE4D):c.682C>G (p.Gln228Glu)]

NM_001104631.2(PDE4D):c.682C>G (p.Gln228Glu)

Gene:

PDE4D:phosphodiesterase 4D [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q11.2

Genomic location:

Preferred name:

NM_001104631.2(PDE4D):c.682C>G (p.Gln228Glu)

HGVS:

NC_000005.10:g.59193502G>C
NG_027957.2:g.1335828C>G
NM_001104631.2:c.682C>GMANE SELECT
NM_001165899.2:c.499C>G
NM_001197218.2:c.490C>G
NM_001197219.2:c.316C>G
NM_001197220.2:c.292C>G
NM_001349241.2:c.469C>G
NM_001349242.2:c.352C>G
NM_001349243.2:c.-13C>G
NM_001364599.1:c.499C>G
NM_001364600.2:c.499C>G
NM_001364602.2:c.490C>G
NM_001364603.1:c.-269C>G
NM_001364604.1:c.-13C>G
NM_006203.5:c.274C>G
NP_001098101.1:p.Gln228Glu
NP_001159371.1:p.Gln167Glu
NP_001184147.1:p.Gln164Glu
NP_001184148.1:p.Gln106Glu
NP_001184149.1:p.Gln98Glu
NP_001336170.1:p.Gln157Glu
NP_001336171.1:p.Gln118Glu
NP_001351528.1:p.Gln167Glu
NP_001351529.1:p.Gln167Glu
NP_001351531.1:p.Gln164Glu
NP_006194.2:p.Gln92Glu
NC_000005.9:g.58489328G>C

Protein change:

Q106E; GLN228GLU

Links:

OMIM: 600129.0005; dbSNP: rs397514468

NCBI 1000 Genomes Browser:

rs397514468

Molecular consequence:

NM_001349243.2:c.-13C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001364603.1:c.-269C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001364604.1:c.-13C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001104631.2:c.682C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001165899.2:c.499C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001197218.2:c.490C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001197219.2:c.316C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001197220.2:c.292C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001349241.2:c.469C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001349242.2:c.352C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001364599.1:c.499C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001364600.2:c.499C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001364602.2:c.490C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_006203.5:c.274C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004293735	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 3, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 24203977, 22464252, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004293735

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 3, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Different mutations in PDE4D associated with developmental disorders with mirror phenotypes.

Lindstrand A, Grigelioniene G, Nilsson D, Pettersson M, Hofmeister W, Anderlid BM, Kant SG, Ruivenkamp CA, Gustavsson P, Valta H, Geiberger S, Topa A, Lagerstedt-Robinson K, Taylan F, Wincent J, Laurell T, Pekkinen M, Nordenskjöld M, Mäkitie O, Nordgren A.

J Med Genet. 2014 Jan;51(1):45-54. doi: 10.1136/jmedgenet-2013-101937. Epub 2013 Nov 7.

PubMed [citation]

PMID:: 24203977

Exome sequencing identifies PDE4D mutations in acrodysostosis.

Lee H, Graham JM Jr, Rimoin DL, Lachman RS, Krejci P, Tompson SW, Nelson SF, Krakow D, Cohn DH.

Am J Hum Genet. 2012 Apr 6;90(4):746-51. doi: 10.1016/j.ajhg.2012.03.004. Epub 2012 Mar 29.

PubMed [citation]

PMID:: 22464252
PMCID:: PMC3322224

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV004293735.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

ClinVar contains an entry for this variant (Variation ID: 30039). For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects PDE4D function (PMID: 24203977). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This missense change has been observed in individual(s) with acrodysostosis (PMID: 22464252). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glutamine, which is neutral and polar, with glutamic acid, which is acidic and polar, at codon 228 of the PDE4D protein (p.Gln228Glu).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 10, 2024

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