NM_001077365.2(POMT1):c.1692G>A (p.Arg564=) AND not specified

Clinical significance:Benign (Last evaluated: Jan 13, 2015)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
6 submissions [Details]
Record status:
current
Accession:
RCV000118032.5

Allele description [Variation Report for NM_001077365.2(POMT1):c.1692G>A (p.Arg564=)]

NM_001077365.2(POMT1):c.1692G>A (p.Arg564=)

Gene:
POMT1:protein O-mannosyltransferase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q34.13
Genomic location:
Preferred name:
NM_001077365.2(POMT1):c.1692G>A (p.Arg564=)
Other names:
p.R586R:AGG>AGA
HGVS:
  • NC_000009.12:g.131520187G>A
  • NG_008896.1:g.22286G>A
  • NM_001077365.2:c.1692G>AMANE SELECT
  • NM_001077366.2:c.1530G>A
  • NM_001136113.2:c.1692G>A
  • NM_001136114.2:c.1341G>A
  • NM_001353193.2:c.1758G>A
  • NM_001353194.2:c.1530G>A
  • NM_001353195.2:c.1341G>A
  • NM_001353196.2:c.1602G>A
  • NM_001353197.2:c.1596G>A
  • NM_001353198.2:c.1596G>A
  • NM_001353199.2:c.1407G>A
  • NM_001353200.2:c.1236G>A
  • NM_001374689.1:c.1680G>A
  • NM_001374690.1:c.1473G>A
  • NM_001374691.1:c.1341G>A
  • NM_001374692.1:c.1341G>A
  • NM_001374693.1:c.1341G>A
  • NM_001374695.1:c.1302G>A
  • NM_007171.3:c.1758G>A
  • NM_007171.4:c.1758G>A
  • NP_001070833.1:p.Arg564=
  • NP_001070834.1:p.Arg510=
  • NP_001129585.1:p.Arg564=
  • NP_001129586.1:p.Arg447=
  • NP_001340122.2:p.Arg586=
  • NP_001340123.1:p.Arg510=
  • NP_001340124.1:p.Arg447=
  • NP_001340125.1:p.Arg534=
  • NP_001340126.2:p.Arg532=
  • NP_001340127.2:p.Arg532=
  • NP_001340128.2:p.Arg469=
  • NP_001340129.1:p.Arg412=
  • NP_001361618.1:p.Arg560=
  • NP_001361619.1:p.Arg491=
  • NP_001361620.1:p.Arg447=
  • NP_001361621.1:p.Arg447=
  • NP_001361622.1:p.Arg447=
  • NP_001361624.1:p.Arg434=
  • NP_009102.3:p.Arg586=
  • NP_009102.4:p.Arg586=
  • LRG_842t1:c.1758G>A
  • LRG_842t2:c.1692G>A
  • LRG_842p1:p.Arg586=
  • LRG_842p2:p.Arg564=
  • NC_000009.11:g.134395574G>A
  • NR_148391.2:n.1726G>A
  • NR_148392.2:n.1944G>A
  • NR_148393.2:n.1865G>A
  • NR_148394.2:n.1619G>A
  • NR_148395.2:n.2017G>A
  • NR_148396.2:n.1651G>A
  • NR_148397.2:n.1776G>A
  • NR_148398.2:n.1731G>A
  • NR_148399.2:n.2257G>A
  • NR_148400.2:n.1856G>A
  • p.Arg586Arg
Links:
dbSNP: rs34954751
NCBI 1000 Genomes Browser:
rs34954751
Molecular consequence:
  • NR_148391.2:n.1726G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148392.2:n.1944G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148393.2:n.1865G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148394.2:n.1619G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148395.2:n.2017G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148396.2:n.1651G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148397.2:n.1776G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148398.2:n.1731G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148399.2:n.2257G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148400.2:n.1856G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001077365.2:c.1692G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001077366.2:c.1530G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001136113.2:c.1692G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001136114.2:c.1341G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001353193.2:c.1758G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001353194.2:c.1530G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001353195.2:c.1341G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001353196.2:c.1602G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001353197.2:c.1596G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001353198.2:c.1596G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001353199.2:c.1407G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001353200.2:c.1236G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001374689.1:c.1680G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001374690.1:c.1473G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001374691.1:c.1341G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001374692.1:c.1341G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001374693.1:c.1341G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001374695.1:c.1302G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_007171.3:c.1758G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_007171.4:c.1758G>A - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
2

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000152353Genetic Services Laboratory, University of Chicagocriteria provided, single submitter
Benign
(Aug 15, 2013)
germlineclinical testing

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

SCV000171150GeneDxcriteria provided, single submitter
Benign
(Mar 21, 2014)
germlineclinical testing

Citation Link,

SCV000269708Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicinecriteria provided, single submitter
Benign
(Jan 13, 2015)
germlineclinical testing

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

SCV000311739PreventionGenetics,PreventionGeneticscriteria provided, single submitter
Benigngermlineclinical testing

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

SCV001799166Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensusno assertion criteria providedBenigngermlineclinical testing

SCV001922494Clinical Genetics,Academic Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria providedBenigngermlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided22not providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
germlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee..

Genet Med. 2008 Apr;10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae.

PubMed [citation]
PMID:
18414213

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020
See all PubMed Citations (3)

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000152353.1

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

From GeneDx, SCV000171150.11

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

From Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, SCV000269708.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testing PubMed (1)

Description

p.Arg586Arg in exon 17 of POMT1: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue and is not located w ithin the splice consensus sequence. It has been identified in 3.4% (291/8600) o f European American chromosomes by the NHLBI Exome Sequencing Project (http://ev s.gs.washington.edu/EVS/; dbSNP rs34954751).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided2not provided2not provided

From PreventionGenetics,PreventionGenetics, SCV000311739.1

#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 Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus, SCV001799166.1

#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,Academic Medical Center - VKGL Data-share Consensus, SCV001922494.1

#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: Oct 6, 2021

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