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NM_001854.4(COL11A1):c.965C>T (p.Pro322Leu) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:
Jan 17, 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:
RCV000179833.17

Allele description [Variation Report for NM_001854.4(COL11A1):c.965C>T (p.Pro322Leu)]

NM_001854.4(COL11A1):c.965C>T (p.Pro322Leu)

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.965C>T (p.Pro322Leu)
HGVS:
  • NC_000001.11:g.103025546G>A
  • NG_008033.2:g.87951C>T
  • NM_001190709.2:c.848C>T
  • NM_001854.4:c.965C>TMANE SELECT
  • NM_080629.3:c.1001C>T
  • NM_080630.4:c.897+670C>T
  • NP_001177638.1:p.Pro283Leu
  • NP_001845.3:p.Pro322Leu
  • NP_542196.2:p.Pro334Leu
  • NC_000001.10:g.103491102G>A
  • NM_001854.3:c.965C>T
  • NR_134980.2:n.1309C>T
Protein change:
P283L
Links:
dbSNP: rs183130583
NCBI 1000 Genomes Browser:
rs183130583
Molecular consequence:
  • NM_080630.4:c.897+670C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001190709.2:c.848C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001854.4:c.965C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_080629.3:c.1001C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_134980.2:n.1309C>T - 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
SCV000232147Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)
Uncertain significance
(Apr 28, 2015)
germlineclinical testing

Citation Link,

SCV001115225Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Jan 17, 2024)
germlineclinical testing

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

SCV001874007GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Uncertain significance
(Feb 28, 2022)
germlineclinical testing

Citation Link

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

Details of each submission

From Eurofins Ntd Llc (ga), SCV000232147.5

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

From Invitae, SCV001115225.5

#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, SCV001874007.3

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

Description

Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not located in the triple helical region, where the majority of pathogenic missense variants occur (Acke et al., 2014; HGMD)

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

Last Updated: Jul 7, 2024