NM_001077365.2(POMT1):c.1047T>C (p.Asp349=) AND not specified

Germline classification:: Benign (5 submissions)
Last evaluated:: Nov 26, 2014
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:: RCV000153753.16

Allele description [Variation Report for NM_001077365.2(POMT1):c.1047T>C (p.Asp349=)]

NM_001077365.2(POMT1):c.1047T>C (p.Asp349=)

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.1047T>C (p.Asp349=)

HGVS:

NC_000009.12:g.131512101T>C
NG_008896.1:g.14200=
NM_001077365.2:c.1047T>CMANE SELECT
NM_001077366.2:c.885T>C
NM_001136113.2:c.1047T>C
NM_001136114.2:c.696T>C
NM_001353193.2:c.1113T>C
NM_001353194.2:c.885T>C
NM_001353195.2:c.696T>C
NM_001353196.2:c.957T>C
NM_001353197.2:c.951T>C
NM_001353198.2:c.951T>C
NM_001353199.2:c.762T>C
NM_001353200.2:c.591T>C
NM_001374689.1:c.1035T>C
NM_001374690.1:c.1047T>C
NM_001374691.1:c.696T>C
NM_001374692.1:c.696T>C
NM_001374693.1:c.824+634T>C
NM_001374695.1:c.657T>C
NM_007171.4:c.1113T>C
NP_001070833.1:p.Asp349=
NP_001070834.1:p.Asp295=
NP_001129585.1:p.Asp349=
NP_001129586.1:p.Asp232=
NP_001340122.2:p.Asp371=
NP_001340123.1:p.Asp295=
NP_001340124.1:p.Asp232=
NP_001340125.1:p.Asp319=
NP_001340126.2:p.Asp317=
NP_001340127.2:p.Asp317=
NP_001340128.2:p.Asp254=
NP_001340129.1:p.Asp197=
NP_001361618.1:p.Asp345=
NP_001361619.1:p.Asp349=
NP_001361620.1:p.Asp232=
NP_001361621.1:p.Asp232=
NP_001361624.1:p.Asp219=
NP_009102.4:p.Asp371=
LRG_842t1:c.1113T>C
LRG_842t2:c.1047T>C
LRG_842p1:p.Asp371=
LRG_842p2:p.Asp349=
NC_000009.11:g.134387488T>C
NP_009102.3:p.(=)
NR_148391.2:n.1081T>C
NR_148392.2:n.1299T>C
NR_148393.2:n.1081T>C
NR_148394.2:n.974T>C
NR_148395.2:n.1233T>C
NR_148396.2:n.867T>C
NR_148397.2:n.1131T>C
NR_148398.2:n.1086T>C
NR_148399.2:n.1473T>C
NR_148400.2:n.1072T>C
p.Asp371Asp

Links:

dbSNP: rs3739494

Molecular consequence:

NM_001374693.1:c.824+634T>C - intron variant - [Sequence Ontology: SO:0001627]
NR_148391.2:n.1081T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148392.2:n.1299T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148393.2:n.1081T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148394.2:n.974T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148395.2:n.1233T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148396.2:n.867T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148397.2:n.1131T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148398.2:n.1086T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148399.2:n.1473T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148400.2:n.1072T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001077365.2:c.1047T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001077366.2:c.885T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001136113.2:c.1047T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001136114.2:c.696T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001353193.2:c.1113T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001353194.2:c.885T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001353195.2:c.696T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001353196.2:c.957T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001353197.2:c.951T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001353198.2:c.951T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001353199.2:c.762T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001353200.2:c.591T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001374689.1:c.1035T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001374690.1:c.1047T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001374691.1:c.696T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001374692.1:c.696T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001374695.1:c.657T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_007171.4:c.1113T>C - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV000203324	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Benign (Apr 23, 2013)	germline	clinical testing	Citation Link,
SCV000269707	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Nov 26, 2014)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001741129	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Benign	germline	clinical testing
SCV001921718	Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Benign	germline	clinical testing
SCV001974152	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Benign	germline	clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	79	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	14	13	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Eurofins Ntd Llc (ga), SCV000203324.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	79	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		79	not provided	not provided	not provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000269707.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	14	not provided	not provided	clinical testing	PubMed (1)

Description

This is a RefSeq error. The reference base (c.1113T) is the minor allele. This a llele (T) has been identified in 5% (411/8600) of European American chromosomes and 26% (1143/4406) of African American chromosomes by the NHLBI Exome Sequencin g Project (http://evs.gs.washington.edu/EVS/; dbSNP rs3739494) and thus meets cr iteria to be classified as benign.

#	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		14	not provided	13	not provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001741129.3

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

From Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001921718.1

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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001974152.1

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

Last Updated: Mar 1, 2026

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