NM_001171.6(ABCC6):c.3883-24G>A AND Autosomal recessive inherited pseudoxanthoma elasticum

Germline classification:: Benign (3 submissions)
Last evaluated:: Dec 5, 2021
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:: RCV000499231.5

Allele description [Variation Report for NM_001171.6(ABCC6):c.3883-24G>A]

NM_001171.6(ABCC6):c.3883-24G>A

Gene:

ABCC6:ATP binding cassette subfamily C member 6 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16p13.11

Genomic location:

Preferred name:

NM_001171.6(ABCC6):c.3883-24G>A

HGVS:

NC_000016.10:g.16155055C>T
NG_007558.3:g.73563G>A
NM_001171.6:c.3883-24G>AMANE SELECT
NM_001351800.1:c.3541-24G>A
LRG_1115t1:c.3883-24G>A
LRG_1115:g.73563G>A
NC_000016.9:g.16248912C>T
NG_007558.2:g.73417G>A
NM_001171.5:c.3883-24G>A

Links:

dbSNP: rs59513011

NCBI 1000 Genomes Browser:

rs59513011

Molecular consequence:

NM_001171.6:c.3883-24G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001351800.1:c.3541-24G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Autosomal recessive inherited pseudoxanthoma elasticum (PXE)
Synonyms:: Gronblad Strandberg syndrome
Identifiers:: MONDO: MONDO:0009925; MedGen: C1275116; Orphanet: 758; OMIM: 264800

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xk90b10.x1 NCI_CGAP_Ut2 Homo sapiens cDNA clone IMAGE:2673979 3', mRNA sequence
xk90b10.x1 NCI_CGAP_Ut2 Homo sapiens cDNA clone IMAGE:2673979 3', mRNA sequence
gi|6463343|gnl|dbEST|3533794|gb|AW1 .1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000589182	PXE International	no assertion criteria provided	Benign (Mar 1, 2021)	germline	research	PubMed (1) [See all records that cite this PMID]
SCV001142458	Reproductive Health Research and Development, BGI Genomics	no assertion criteria provided	Likely benign (Jan 6, 2020)	germline	curation
SCV002524261	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Dec 5, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000589182

PXE International

no assertion criteria provided

Benign
(Mar 1, 2021)

germline

research

PubMed (1)
[See all records that cite this PMID]

SCV001142458

Reproductive Health Research and Development, BGI Genomics

no assertion criteria provided

Likely benign
(Jan 6, 2020)

germline

curation

SCV002524261

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Dec 5, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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	curation
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	research

Citations

PubMed

Molecular genetics of pseudoxanthoma elasticum: type and frequency of mutations in ABCC6.

Miksch S, Lumsden A, Guenther UP, Foernzler D, Christen-Zäch S, Daugherty C, Ramesar RK, Lebwohl M, Hohl D, Neldner KH, Lindpaintner K, Richards RI, Struk B.

Hum Mutat. 2005 Sep;26(3):235-48.

PubMed [citation]

PMID:: 16086317

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 PXE International, SCV000589182.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	PubMed (1)

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

From Reproductive Health Research and Development, BGI Genomics, SCV001142458.1

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

Description

NG_007558.2(NM_001171.5):c.3883-24G>A in the ABCC6 gene has an allele frequency of 0.014 in South Asian subpopulation in the gnomAD database. Benign computational verdict because benign prediction from DANN. The variant was identified in a pseudoxanthoma elasticum patient (PMID: 16127278). Taken together, we interprete this variant as Benign/Likely benign variant. ACMG/AMP criteria applied: BS1, BP4.

#	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

From Genome-Nilou Lab, SCV002524261.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 16, 2024

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