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NM_080680.3(COL11A2):c.1607G>A (p.Arg536Gln) AND Larsen-like syndrome, B3GAT3 type

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 2, 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:
RCV000171392.1

Allele description

NM_080680.3(COL11A2):c.1607G>A (p.Arg536Gln)

Gene:
COL11A2:collagen type XI alpha 2 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6p21.32
Genomic location:
Preferred name:
NM_080680.3(COL11A2):c.1607G>A (p.Arg536Gln)
HGVS:
  • NC_000006.12:g.33179077C>T
  • NG_011589.1:g.18392G>A
  • NM_080679.3:c.1286G>A
  • NM_080680.3:c.1607G>AMANE SELECT
  • NM_080681.3:c.1349G>A
  • NP_542410.2:p.Arg429Gln
  • NP_542411.2:p.Arg536Gln
  • NP_542412.2:p.Arg450Gln
  • NC_000006.11:g.33146854C>T
Protein change:
R429Q
Links:
dbSNP: rs770888294
NCBI 1000 Genomes Browser:
rs770888294
Molecular consequence:
  • NM_080679.3:c.1286G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_080680.3:c.1607G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_080681.3:c.1349G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Larsen-like syndrome, B3GAT3 type
Synonyms:
LARSEN SYNDROME, AUTOSOMAL RECESSIVE; Multiple joint dislocations, short stature, craniofacial dysmorphism, and congenital heart defects; MULTIPLE JOINT DISLOCATIONS, SHORT STATURE, AND CRANIOFACIAL DYSMORPHISM WITH OR WITHOUT CONGENITAL HEART DEFECTS
Identifiers:
MONDO: MONDO:0009511; MedGen: C3278404; Orphanet: 284139; OMIM: 245600

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000221589Developmental Genetics Unit, King Faisal Specialist Hospital & Research Centre
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Nov 2, 2016) 		germlineresearch

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providedyesresearch

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 Developmental Genetics Unit, King Faisal Specialist Hospital & Research Centre, SCV000221589.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providedyesresearch PubMed (1)

Description

We have previously reported this variant as likely pathogenic in a child with Larsen syndrome features based on a) complete absence in public and local databases, b) potential compatibility with the phenotype, c) in silico prediction. However, we have now received new data indicating the presence of a cousin with an identical phenotype who was found to be homozygous for NM_007255.1:c.808C>T:p.R270C (NC_000005.9:g.177035995C>T). Since this a published variant that causes autosomal recessive Larsen syndrome, we believe it is the most likely cause of the phenotype and we now reclassify our original COL11A2 variant into VOUS.

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

Last Updated: Jul 16, 2023