NM_001077365.2(POMT1):c.868C>T (p.Arg290Trp) AND not specified

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Aug 31, 2017
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000332052.14

Allele description [Variation Report for NM_001077365.2(POMT1):c.868C>T (p.Arg290Trp)]

NM_001077365.2(POMT1):c.868C>T (p.Arg290Trp)

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.868C>T (p.Arg290Trp)

HGVS:

NC_000009.12:g.131511349C>T
NG_008896.1:g.13448C>T
NM_001077365.2:c.868C>TMANE SELECT
NM_001077366.2:c.706C>T
NM_001136113.2:c.868C>T
NM_001136114.2:c.517C>T
NM_001353193.2:c.934C>T
NM_001353194.2:c.706C>T
NM_001353195.2:c.517C>T
NM_001353196.2:c.778C>T
NM_001353197.2:c.772C>T
NM_001353198.2:c.772C>T
NM_001353199.2:c.583C>T
NM_001353200.2:c.412C>T
NM_001374689.1:c.851C>T
NM_001374690.1:c.868C>T
NM_001374691.1:c.517C>T
NM_001374692.1:c.517C>T
NM_001374693.1:c.706C>T
NM_001374695.1:c.478C>T
NM_007171.4:c.934C>T
NP_001070833.1:p.Arg290Trp
NP_001070834.1:p.Arg236Trp
NP_001129585.1:p.Arg290Trp
NP_001129586.1:p.Arg173Trp
NP_001340122.2:p.Arg312Trp
NP_001340123.1:p.Arg236Trp
NP_001340124.1:p.Arg173Trp
NP_001340125.1:p.Arg260Trp
NP_001340126.2:p.Arg258Trp
NP_001340127.2:p.Arg258Trp
NP_001340128.2:p.Arg195Trp
NP_001340129.1:p.Arg138Trp
NP_001361618.1:p.Ser284Leu
NP_001361619.1:p.Arg290Trp
NP_001361620.1:p.Arg173Trp
NP_001361621.1:p.Arg173Trp
NP_001361622.1:p.Arg236Trp
NP_001361624.1:p.Arg160Trp
NP_009102.3:p.Arg312Trp
NP_009102.4:p.Arg312Trp
LRG_842t1:c.934C>T
LRG_842t2:c.868C>T
LRG_842p1:p.Arg312Trp
LRG_842p2:p.Arg290Trp
NC_000009.11:g.134386736C>T
NM_007171.3:c.934C>T
NR_148391.2:n.902C>T
NR_148392.2:n.1120C>T
NR_148393.2:n.902C>T
NR_148394.2:n.790C>T
NR_148395.2:n.1054C>T
NR_148396.2:n.683C>T
NR_148397.2:n.947C>T
NR_148398.2:n.902C>T
NR_148399.2:n.1294C>T
NR_148400.2:n.888C>T

Protein change:

R138W

Links:

dbSNP: rs886042627

NCBI 1000 Genomes Browser:

rs886042627

Molecular consequence:

NM_001077365.2:c.868C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001077366.2:c.706C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001136113.2:c.868C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001136114.2:c.517C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353193.2:c.934C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353194.2:c.706C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353195.2:c.517C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353196.2:c.778C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353197.2:c.772C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353198.2:c.772C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353199.2:c.583C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353200.2:c.412C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374689.1:c.851C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374690.1:c.868C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374691.1:c.517C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374692.1:c.517C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374693.1:c.706C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374695.1:c.478C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_007171.4:c.934C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_148391.2:n.902C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148392.2:n.1120C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148393.2:n.902C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148394.2:n.790C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148395.2:n.1054C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148396.2:n.683C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148397.2:n.947C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148398.2:n.902C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148399.2:n.1294C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148400.2:n.888C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000596533	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Dec 28, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000712538	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Uncertain significance (Aug 31, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000596533

Genetic Services Laboratory, University of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Dec 28, 2015)

germline

clinical testing

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

SCV000712538

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Uncertain significance
(Aug 31, 2017)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	2	1	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical 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

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

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000596533.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000712538.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	PubMed (1)

Description

The p.Arg312Trp variant in POMT1 has not been previously reported in individuals with myopathy but has been identified in 5 /277130 chromosomes by the Genome Ag gregation Database (gnomAD, http://gnomad.broadinstitute.org). Computational pre diction tools and conservation analysis suggest that the p.Arg312Trp variant may impact the protein, though this information is not predictive enough to determi ne pathogenicity. In summary, the clinical significance of the p.Arg312Trp varia nt is uncertain.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		2	not provided	1	not provided

Last Updated: Sep 29, 2024

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