NM_001077365.2(POMT1):c.1856C>T (p.Ala619Val) AND not provided

Germline classification:: Benign (2 submissions)
Last evaluated:: Nov 1, 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:: RCV000712821.7

Allele description [Variation Report for NM_001077365.2(POMT1):c.1856C>T (p.Ala619Val)]

NM_001077365.2(POMT1):c.1856C>T (p.Ala619Val)

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.1856C>T (p.Ala619Val)

HGVS:

NC_000009.12:g.131522077C>T
NG_008896.1:g.24176C>T
NM_001077365.2:c.1856C>TMANE SELECT
NM_001077366.2:c.1694C>T
NM_001136113.2:c.1856C>T
NM_001136114.2:c.1505C>T
NM_001353193.2:c.1922C>T
NM_001353194.2:c.1694C>T
NM_001353195.2:c.1505C>T
NM_001353196.2:c.1766C>T
NM_001353197.2:c.1760C>T
NM_001353198.2:c.1760C>T
NM_001353199.2:c.1571C>T
NM_001353200.2:c.1400C>T
NM_001374689.1:c.1844C>T
NM_001374690.1:c.1637C>T
NM_001374691.1:c.1505C>T
NM_001374692.1:c.1505C>T
NM_001374693.1:c.1505C>T
NM_001374695.1:c.1466C>T
NM_007171.4:c.1922C>T
NP_001070833.1:p.Ala619Val
NP_001070834.1:p.Ala565Val
NP_001129585.1:p.Ala619Val
NP_001129586.1:p.Ala502Val
NP_001340122.2:p.Ala641Val
NP_001340123.1:p.Ala565Val
NP_001340124.1:p.Ala502Val
NP_001340125.1:p.Ala589Val
NP_001340126.2:p.Ala587Val
NP_001340127.2:p.Ala587Val
NP_001340128.2:p.Ala524Val
NP_001340129.1:p.Ala467Val
NP_001361618.1:p.Ala615Val
NP_001361619.1:p.Ala546Val
NP_001361620.1:p.Ala502Val
NP_001361621.1:p.Ala502Val
NP_001361622.1:p.Ala502Val
NP_001361624.1:p.Ala489Val
NP_009102.3:p.Ala641Val
NP_009102.4:p.Ala641Val
LRG_842t1:c.1922C>T
LRG_842t2:c.1856C>T
LRG_842p1:p.Ala641Val
LRG_842p2:p.Ala619Val
NC_000009.11:g.134397464C>T
NM_007171.3:c.1922C>T
NR_148391.2:n.1890C>T
NR_148392.2:n.2108C>T
NR_148393.2:n.2029C>T
NR_148394.2:n.1783C>T
NR_148395.2:n.2181C>T
NR_148396.2:n.1815C>T
NR_148397.2:n.1940C>T
NR_148398.2:n.1895C>T
NR_148399.2:n.2421C>T
NR_148400.2:n.2020C>T

Protein change:

A467V

Links:

dbSNP: rs12115566

NCBI 1000 Genomes Browser:

rs12115566

Molecular consequence:

NM_001077365.2:c.1856C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001077366.2:c.1694C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001136113.2:c.1856C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001136114.2:c.1505C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353193.2:c.1922C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353194.2:c.1694C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353195.2:c.1505C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353196.2:c.1766C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353197.2:c.1760C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353198.2:c.1760C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353199.2:c.1571C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353200.2:c.1400C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374689.1:c.1844C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374690.1:c.1637C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374691.1:c.1505C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374692.1:c.1505C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374693.1:c.1505C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374695.1:c.1466C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_007171.4:c.1922C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_148391.2:n.1890C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148392.2:n.2108C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148393.2:n.2029C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148394.2:n.1783C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148395.2:n.2181C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148396.2:n.1815C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148397.2:n.1940C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148398.2:n.1895C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148399.2:n.2421C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148400.2:n.2020C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV000843355	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (Nov 1, 2017)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 16575835, 17878207, 18647264, 26467025
SCV001945140	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Mar 3, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000843355

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Benign
(Nov 1, 2017)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV001945140

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(Mar 3, 2015)

germline

clinical testing

Citation Link

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	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

The expanding phenotype of POMT1 mutations: from Walker-Warburg syndrome to congenital muscular dystrophy, microcephaly, and mental retardation.

van Reeuwijk J, Maugenre S, van den Elzen C, Verrips A, Bertini E, Muntoni F, Merlini L, Scheffer H, Brunner HG, Guicheney P, van Bokhoven H.

Hum Mutat. 2006 May;27(5):453-9.

PubMed [citation]

PMID:: 16575835

Refining genotype phenotype correlations in muscular dystrophies with defective glycosylation of dystroglycan.

Godfrey C, Clement E, Mein R, Brockington M, Smith J, Talim B, Straub V, Robb S, Quinlivan R, Feng L, Jimenez-Mallebrera C, Mercuri E, Manzur AY, Kinali M, Torelli S, Brown SC, Sewry CA, Bushby K, Topaloglu H, North K, Abbs S, Muntoni F.

Brain. 2007 Oct;130(Pt 10):2725-35. Epub 2007 Sep 18.

PubMed [citation]

PMID:: 17878207

See all PubMed Citations (4)

Details of each submission

From Athena Diagnostics, SCV000843355.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

#	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

From GeneDx, SCV001945140.2

#	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: May 7, 2024

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