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NM_000302.4(PLOD1):c.976-6C>A AND Ehlers-Danlos syndrome, kyphoscoliotic type 1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 30, 2016
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:
RCV000542619.8

Allele description [Variation Report for NM_000302.4(PLOD1):c.976-6C>A]

NM_000302.4(PLOD1):c.976-6C>A

Gene:
PLOD1:procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p36.22
Genomic location:
Preferred name:
NM_000302.4(PLOD1):c.976-6C>A
HGVS:
  • NC_000001.11:g.11960640C>A
  • NG_008159.1:g.30952C>A
  • NM_000302.4:c.976-6C>AMANE SELECT
  • NM_001316320.2:c.1117-6C>A
  • NC_000001.10:g.12020697C>A
  • NM_000302.3:c.976-6C>A
Links:
dbSNP: rs200825919
NCBI 1000 Genomes Browser:
rs200825919
Molecular consequence:
  • NM_000302.4:c.976-6C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001316320.2:c.1117-6C>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Ehlers-Danlos syndrome, kyphoscoliotic type 1 (EDSKSCL1)
Synonyms:
EHLERS-DANLOS SYNDROME, TYPE VIA; EHLERS-DANLOS SYNDROME, OCULAR-SCOLIOTIC TYPE; Nevo syndrome; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0016002; MedGen: C0268342; Orphanet: 1900; OMIM: 225400

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000631745Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 30, 2016) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000631745.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

In summary, this is a novel intronic change with uncertain impact on splicing. It has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may alter RNA splicing, but this prediction has not been confirmed by published transcriptional studies. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a PLOD1-related disease. This sequence change falls in intron 9 of the PLOD1 gene. It does not directly change the encoded amino acid sequence of the PLOD1 protein.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 28, 2024