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NM_000302.4(PLOD1):c.1562G>A (p.Trp521Ter) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 1, 2017
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:
RCV000626656.2

Allele description [Variation Report for NM_000302.4(PLOD1):c.1562G>A (p.Trp521Ter)]

NM_000302.4(PLOD1):c.1562G>A (p.Trp521Ter)

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.1562G>A (p.Trp521Ter)
HGVS:
  • NC_000001.11:g.11965571G>A
  • NG_008159.1:g.35883G>A
  • NM_000302.4:c.1562G>AMANE SELECT
  • NM_001316320.2:c.1703G>A
  • NP_000293.2:p.Trp521Ter
  • NP_001303249.1:p.Trp568Ter
  • NC_000001.10:g.12025628G>A
  • NM_000302.3:c.1562G>A
Protein change:
W521*
Links:
dbSNP: rs1057518879
NCBI 1000 Genomes Browser:
rs1057518879
Molecular consequence:
  • NM_000302.4:c.1562G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001316320.2:c.1703G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Short chin
Synonyms:
Small chin
Identifiers:
MedGen: C3697248; Human Phenotype Ontology: HP:0000331
Name:
Feeding difficulties
Identifiers:
MedGen: C0232466; Human Phenotype Ontology: HP:0011968
Name:
Bilateral cryptorchidism
Identifiers:
MedGen: C0431663; Human Phenotype Ontology: HP:0008689
Name:
Hypoplasia of scrotum
Identifiers:
MedGen: C0431659
Name:
Joint hypermobility
Identifiers:
MedGen: C1844820; Human Phenotype Ontology: HP:0001382
Name:
Generalized neonatal hypotonia
Identifiers:
MedGen: C1845123; Human Phenotype Ontology: HP:0008935

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000747358Centre for Mendelian Genomics, University Medical Centre Ljubljana
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Jan 1, 2017) 		unknownclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

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 Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV000747358.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 10, 2023