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NM_001734.5(C1S):c.1016C>T (p.Ser339Leu) AND Ehlers-Danlos syndrome, periodontal type 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 20, 2023
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:
RCV004763430.2

Allele description [Variation Report for NM_001734.5(C1S):c.1016C>T (p.Ser339Leu)]

NM_001734.5(C1S):c.1016C>T (p.Ser339Leu)

Gene:
C1S:complement C1s [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12p13.31
Genomic location:
Preferred name:
NM_001734.5(C1S):c.1016C>T (p.Ser339Leu)
HGVS:
  • NC_000012.12:g.7067067C>T
  • NG_011694.1:g.11392C>T
  • NM_001346850.2:c.515C>T
  • NM_001734.5:c.1016C>TMANE SELECT
  • NM_201442.4:c.1016C>T
  • NP_001333779.1:p.Ser172Leu
  • NP_001725.1:p.Ser339Leu
  • NP_001725.1:p.Ser339Leu
  • NP_958850.1:p.Ser339Leu
  • LRG_25t1:c.1016C>T
  • LRG_25:g.11392C>T
  • LRG_25p1:p.Ser339Leu
  • NC_000012.11:g.7174371C>T
  • NM_001734.3:c.1016C>T
Protein change:
S172L
Molecular consequence:
  • NM_001346850.2:c.515C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001734.5:c.1016C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_201442.4:c.1016C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Ehlers-Danlos syndrome, periodontal type 2
Identifiers:
MONDO: MONDO:0014954; MedGen: C4310681; OMIM: 617174

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005373518Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(May 20, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot 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 Neuberg Centre For Genomic Medicine, NCGM, SCV005373518.2

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

Description

The observed missense c.1016C>T(p.Ser339Leu) variant in C1S gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is present with an allele frequency of 0.002% in gnomAD Exomes database. This variant has been submitted to the ClinVar database as Uncertain Significance. Computational evidence (Polyphen - possibly damaging, SIFT - Tolerated and MutationTaster -disease causing) predicts conflicting evidence on protein structure and function for this variant. The reference amino acid is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Ser at position 339 is changed to a Leu changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Uncertain Significance (VUS).

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

Last Updated: Nov 24, 2024