U.S. flag

An official website of the United States government

NM_000093.5(COL5A1):c.5338C>T (p.Pro1780Ser) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 9, 2018
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:
RCV000198444.10

Allele description [Variation Report for NM_000093.5(COL5A1):c.5338C>T (p.Pro1780Ser)]

NM_000093.5(COL5A1):c.5338C>T (p.Pro1780Ser)

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.5338C>T (p.Pro1780Ser)
Other names:
p.P1780S:CCC>TCC
HGVS:
  • NC_000009.12:g.134835172C>T
  • NG_008030.1:g.198367C>T
  • NM_000093.5:c.5338C>TMANE SELECT
  • NM_001278074.1:c.5338C>T
  • NP_000084.3:p.Pro1780Ser
  • NP_000084.3:p.Pro1780Ser
  • NP_001265003.1:p.Pro1780Ser
  • LRG_737t1:c.5338C>T
  • LRG_737t2:c.5338C>T
  • LRG_737:g.198367C>T
  • LRG_737p1:p.Pro1780Ser
  • LRG_737p2:p.Pro1780Ser
  • NC_000009.11:g.137727018C>T
  • NM_000093.3:c.5338C>T
  • NM_000093.4:c.5338C>T
Protein change:
P1780S
Links:
dbSNP: rs781230603
NCBI 1000 Genomes Browser:
rs781230603
Molecular consequence:
  • NM_000093.5:c.5338C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001278074.1:c.5338C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000249857GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Feb 9, 2018) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000249857.11

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The P1780S variant in the COL5A1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. This variant is observed in 7/33,580 alleles (0.02%) from individuals of Latino background, and 8/245,584 global alleles (0.003%), in large population cohorts (Lek et al., 2016). The P1780S variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. In-silico analyses, including protein predictors and evolutionary conservation, support a deleterious effect. We interpret P1780S as a variant of uncertain significance.

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

Last Updated: Nov 3, 2024