NM_001077365.2(POMT1):c.1838G>A (p.Arg613His) AND not provided

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Feb 25, 2022
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:: RCV000726099.9

Allele description [Variation Report for NM_001077365.2(POMT1):c.1838G>A (p.Arg613His)]

NM_001077365.2(POMT1):c.1838G>A (p.Arg613His)

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.1838G>A (p.Arg613His)

HGVS:

NC_000009.12:g.131522059G>A
NG_008896.1:g.24158G>A
NM_001077365.2:c.1838G>AMANE SELECT
NM_001077366.2:c.1676G>A
NM_001136113.2:c.1838G>A
NM_001136114.2:c.1487G>A
NM_001353193.2:c.1904G>A
NM_001353194.2:c.1676G>A
NM_001353195.2:c.1487G>A
NM_001353196.2:c.1748G>A
NM_001353197.2:c.1742G>A
NM_001353198.2:c.1742G>A
NM_001353199.2:c.1553G>A
NM_001353200.2:c.1382G>A
NM_001374689.1:c.1826G>A
NM_001374690.1:c.1619G>A
NM_001374691.1:c.1487G>A
NM_001374692.1:c.1487G>A
NM_001374693.1:c.1487G>A
NM_001374695.1:c.1448G>A
NM_007171.4:c.1904G>A
NP_001070833.1:p.Arg613His
NP_001070834.1:p.Arg559His
NP_001129585.1:p.Arg613His
NP_001129586.1:p.Arg496His
NP_001340122.2:p.Arg635His
NP_001340123.1:p.Arg559His
NP_001340124.1:p.Arg496His
NP_001340125.1:p.Arg583His
NP_001340126.2:p.Arg581His
NP_001340127.2:p.Arg581His
NP_001340128.2:p.Arg518His
NP_001340129.1:p.Arg461His
NP_001361618.1:p.Arg609His
NP_001361619.1:p.Arg540His
NP_001361620.1:p.Arg496His
NP_001361621.1:p.Arg496His
NP_001361622.1:p.Arg496His
NP_001361624.1:p.Arg483His
NP_009102.3:p.Arg635His
NP_009102.4:p.Arg635His
LRG_842t1:c.1904G>A
LRG_842t2:c.1838G>A
LRG_842p1:p.Arg635His
LRG_842p2:p.Arg613His
NC_000009.11:g.134397446G>A
NM_007171.3:c.1904G>A
NR_148391.2:n.1872G>A
NR_148392.2:n.2090G>A
NR_148393.2:n.2011G>A
NR_148394.2:n.1765G>A
NR_148395.2:n.2163G>A
NR_148396.2:n.1797G>A
NR_148397.2:n.1922G>A
NR_148398.2:n.1877G>A
NR_148399.2:n.2403G>A
NR_148400.2:n.2002G>A

Protein change:

R461H

Links:

dbSNP: rs147601415

NCBI 1000 Genomes Browser:

rs147601415

Molecular consequence:

NM_001077365.2:c.1838G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001077366.2:c.1676G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001136113.2:c.1838G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001136114.2:c.1487G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353193.2:c.1904G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353194.2:c.1676G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353195.2:c.1487G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353196.2:c.1748G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353197.2:c.1742G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353198.2:c.1742G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353199.2:c.1553G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353200.2:c.1382G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374689.1:c.1826G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374690.1:c.1619G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374691.1:c.1487G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374692.1:c.1487G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374693.1:c.1487G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374695.1:c.1448G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_007171.4:c.1904G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_148391.2:n.1872G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148392.2:n.2090G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148393.2:n.2011G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148394.2:n.1765G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148395.2:n.2163G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148396.2:n.1797G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148397.2:n.1922G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148398.2:n.1877G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148399.2:n.2403G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148400.2:n.2002G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000341978	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL ClinVar v180209 classification definitions)	Uncertain significance (Feb 28, 2018)	germline	clinical testing	Citation Link,
SCV000515736	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Feb 25, 2022)	germline	clinical testing	Citation Link,
SCV003811821	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jun 4, 2019)	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

SCV000341978

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL ClinVar v180209 classification definitions)

Uncertain significance
(Feb 28, 2018)

germline

clinical testing

Citation Link,

SCV000515736

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Feb 25, 2022)

germline

clinical testing

Citation Link,

SCV003811821

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jun 4, 2019)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	3	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

Details of each submission

From Eurofins Ntd Llc (ga), SCV000341978.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		3	not provided	not provided	not provided

From GeneDx, SCV000515736.6

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 30564623)

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

From Revvity Omics, Revvity, SCV003811821.2

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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