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NM_001854.4(COL11A1):c.5198G>A (p.Arg1733His) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (6 submissions)
Last evaluated:
Jan 31, 2024
Review status:
criteria provided, conflicting classifications
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:
RCV000179660.20

Allele description [Variation Report for NM_001854.4(COL11A1):c.5198G>A (p.Arg1733His)]

NM_001854.4(COL11A1):c.5198G>A (p.Arg1733His)

Genes:
LOC126805814:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:103344928-103346127 [Gene]
COL11A1:collagen type XI alpha 1 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p21.1
Genomic location:
Preferred name:
NM_001854.4(COL11A1):c.5198G>A (p.Arg1733His)
HGVS:
  • NC_000001.11:g.102879759C>T
  • NG_008033.2:g.233738G>A
  • NM_001190709.2:c.5081G>A
  • NM_001854.4:c.5198G>AMANE SELECT
  • NM_080629.3:c.5234G>A
  • NM_080630.4:c.4850G>A
  • NP_001177638.1:p.Arg1694His
  • NP_001845.3:p.Arg1733His
  • NP_542196.2:p.Arg1745His
  • NP_542196.2:p.Arg1745His
  • NP_542197.3:p.Arg1617His
  • NC_000001.10:g.103345315C>T
  • NM_001854.3:c.5198G>A
  • NM_080629.2:c.5234G>A
  • NR_134980.2:n.5558G>A
Protein change:
R1617H
Links:
dbSNP: rs140250347
NCBI 1000 Genomes Browser:
rs140250347
Molecular consequence:
  • NM_001190709.2:c.5081G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001854.4:c.5198G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_080629.3:c.5234G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_080630.4:c.4850G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_134980.2:n.5558G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000231943Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)
Uncertain significance
(Nov 16, 2016)
germlineclinical testing

Citation Link,

SCV001068940Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Jan 31, 2024)
germlineclinical testing

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

SCV001143580Athena Diagnostics
criteria provided, single submitter

(Athena Diagnostics Criteria)
Benign
(Jun 27, 2019)
germlineclinical testing

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

SCV001780620GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Likely benign
(Apr 12, 2022)
germlineclinical testing

Citation Link,

SCV001979877Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Likely benigngermlineclinical testing

SCV001980101Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Likely benigngermlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

Details of each submission

From Eurofins Ntd Llc (ga), SCV000231943.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From Invitae, SCV001068940.6

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

From Athena Diagnostics, SCV001143580.1

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

From GeneDx, SCV001780620.2

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

Description

See Variant Classification Assertion Criteria.

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

From Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus, SCV001979877.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001980101.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 15, 2024