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NM_000093.5(COL5A1):c.4607C>T (p.Pro1536Leu) AND Aortic root aneurysm

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 17, 2020
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:
RCV001263364.9

Allele description [Variation Report for NM_000093.5(COL5A1):c.4607C>T (p.Pro1536Leu)]

NM_000093.5(COL5A1):c.4607C>T (p.Pro1536Leu)

Genes:
COL5A1:collagen type V alpha 1 chain [Gene - OMIM - HGNC]
LOC101448202:uncharacterized LOC101448202 [Gene]
Variant type:
single nucleotide variant
Cytogenetic location:
9q34.3
Genomic location:
Preferred name:
NM_000093.5(COL5A1):c.4607C>T (p.Pro1536Leu)
HGVS:
  • NC_000009.12:g.134822149C>T
  • NG_008030.1:g.185344C>T
  • NM_000093.5:c.4607C>TMANE SELECT
  • NM_001278074.1:c.4607C>T
  • NP_000084.3:p.Pro1536Leu
  • NP_000084.3:p.Pro1536Leu
  • NP_001265003.1:p.Pro1536Leu
  • LRG_737t1:c.4607C>T
  • LRG_737t2:c.4607C>T
  • LRG_737:g.185344C>T
  • LRG_737p1:p.Pro1536Leu
  • LRG_737p2:p.Pro1536Leu
  • NC_000009.11:g.137713995C>T
  • NM_000093.3:c.4607C>T
  • NM_000093.4:c.4607C>T
Protein change:
P1536L
Links:
dbSNP: rs761837954
NCBI 1000 Genomes Browser:
rs761837954
Molecular consequence:
  • NM_000093.5:c.4607C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001278074.1:c.4607C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Aortic root aneurysm
Synonyms:
Aneurysm of aortic root
Identifiers:
MedGen: C1298820; Human Phenotype Ontology: HP:0002616

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001441406New York Genome Center - CSER-NYCKidSeq
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Uncertain significance
(Mar 17, 2020) 		maternalclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedmaternalyes1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center - CSER-NYCKidSeq, SCV001441406.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The c.4607C>T (p.Pro1536Leu) variant identified in the COL5A1 gene substitutes a very well conserved Proline for Leucine at amino acid 1536/1839 (coding exon 59/66). This variant is found with low frequency in gnomAD (15 heterozygotes, 0 homozygotes; allele frequency: 5.32e-5) suggesting it is not a common benign variant in the populations represented in this database. In silico algorithms predict this variant to be Deleterious (Provean; score: -4.51) and Damaging (SIFT; score: 0.034) to the function of the canonical transcript. This variant is reported in ClinVar (VarID:459697) as a Variant of Uncertain Significance and to our current knowledge has not been reported in affected individuals in the literature. The p.Pro1536 residue is within the triple-helical region of the protein. Given the lack of compelling information for its pathogenicity, the c.4607C>T (p.Pro1536Leu) variant identified in the COL5A1 gene is reported here as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1maternalyes1not providednot provided1not providednot providednot provided

Last Updated: Oct 13, 2024