NM_016953.4(PDE11A):c.2268_2272del (p.Ser757fs) AND Pigmented nodular adrenocortical disease, primary, 2

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: May 4, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000490402.2

Allele description [Variation Report for NM_016953.4(PDE11A):c.2268_2272del (p.Ser757fs)]

NM_016953.4(PDE11A):c.2268_2272del (p.Ser757fs)

Genes:

PDE11A-AS1:PDE11A antisense RNA 1 [Gene - HGNC]
PDE11A:phosphodiesterase 11A [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2q31.2

Genomic location:

Preferred name:

NM_016953.4(PDE11A):c.2268_2272del (p.Ser757fs)

HGVS:

NC_000002.12:g.177697408_177697412del
NG_012168.2:g.415931_415935del
NM_001077196.2:c.936_940del
NM_001077197.2:c.1518_1522del
NM_001077358.2:c.1194_1198del
NM_016953.4:c.2268_2272delMANE SELECT
NP_001070664.1:p.Ser313fs
NP_001070665.1:p.Ser507fs
NP_001070826.1:p.Ser399fs
NP_058649.3:p.Ser757fs
NC_000002.11:g.178562136_178562140del
NC_000002.12:g.177697405_177697409delAGGAC
NM_001077196.1:c.936_940delGTCCT

Protein change:

S313fs

Links:

dbSNP: rs769235876

NCBI 1000 Genomes Browser:

rs769235876

Molecular consequence:

NM_001077196.2:c.936_940del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001077197.2:c.1518_1522del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001077358.2:c.1194_1198del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_016953.4:c.2268_2272del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Pigmented nodular adrenocortical disease, primary, 2 (PPNAD2)
Synonyms:: CUSHING SYNDROME, ADRENAL, DUE TO PPNAD2; PIGMENTED MICRONODULAR ADRENOCORTICAL DISEASE, PRIMARY, 2
Identifiers:: MONDO: MONDO:0012505; MedGen: C1864851; Orphanet: 189439; OMIM: 610475

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000267439	Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 18, 2016)	germline	reference population	PubMed (2) [See all records that cite these PMIDs] 16767104, 25741868
SCV002518769	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2019)	Pathogenic (May 4, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000267439

Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 18, 2016)

germline

reference population

PubMed (2)
[See all records that cite these PMIDs]

SCV002518769

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2019)

Pathogenic
(May 4, 2022)

germline

clinical testing

Citation Link

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
East Asian	germline	unknown	1	not provided	not provided	not provided	not provided	reference population

Citations

PubMed

A genome-wide scan identifies mutations in the gene encoding phosphodiesterase 11A4 (PDE11A) in individuals with adrenocortical hyperplasia.

Horvath A, Boikos S, Giatzakis C, Robinson-White A, Groussin L, Griffin KJ, Stein E, Levine E, Delimpasi G, Hsiao HP, Keil M, Heyerdahl S, Matyakhina L, Libè R, Fratticci A, Kirschner LS, Cramer K, Gaillard RC, Bertagna X, Carney JA, Bertherat J, Bossis I, et al.

Nat Genet. 2006 Jul;38(7):794-800. Epub 2006 Jun 11.

PubMed [citation]

PMID:: 16767104

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center, SCV000267439.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	East Asian	1	not provided	not provided	reference population	PubMed (2)

#	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		1	not provided	not provided	not provided

From Mendelics, SCV002518769.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	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: May 28, 2022

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