NM_001077365.2(POMT1):c.2059G>A (p.Ala687Thr) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 31, 2018
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV000764808.3

Allele description [Variation Report for NM_001077365.2(POMT1):c.2059G>A (p.Ala687Thr)]

NM_001077365.2(POMT1):c.2059G>A (p.Ala687Thr)

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.2059G>A (p.Ala687Thr)

HGVS:

NC_000009.12:g.131522987G>A
NG_008896.1:g.25086G>A
NM_001077365.2:c.2059G>AMANE SELECT
NM_001077366.2:c.1897G>A
NM_001136113.2:c.2059G>A
NM_001136114.2:c.1708G>A
NM_001353193.2:c.2125G>A
NM_001353194.2:c.1897G>A
NM_001353195.2:c.1708G>A
NM_001353196.2:c.1969G>A
NM_001353197.2:c.1963G>A
NM_001353198.2:c.1963G>A
NM_001353199.2:c.1774G>A
NM_001353200.2:c.1603G>A
NM_001374689.1:c.2047G>A
NM_001374690.1:c.1840G>A
NM_001374691.1:c.1708G>A
NM_001374692.1:c.1708G>A
NM_001374693.1:c.1708G>A
NM_001374695.1:c.1669G>A
NM_007171.4:c.2125G>A
NP_001070833.1:p.Ala687Thr
NP_001070834.1:p.Ala633Thr
NP_001129585.1:p.Ala687Thr
NP_001129586.1:p.Ala570Thr
NP_001340122.2:p.Ala709Thr
NP_001340123.1:p.Ala633Thr
NP_001340124.1:p.Ala570Thr
NP_001340125.1:p.Ala657Thr
NP_001340126.2:p.Ala655Thr
NP_001340127.2:p.Ala655Thr
NP_001340128.2:p.Ala592Thr
NP_001340129.1:p.Ala535Thr
NP_001361618.1:p.Ala683Thr
NP_001361619.1:p.Ala614Thr
NP_001361620.1:p.Ala570Thr
NP_001361621.1:p.Ala570Thr
NP_001361622.1:p.Ala570Thr
NP_001361624.1:p.Ala557Thr
NP_009102.3:p.Ala709Thr
NP_009102.4:p.Ala709Thr
LRG_842t1:c.2125G>A
LRG_842t2:c.2059G>A
LRG_842p1:p.Ala709Thr
LRG_842p2:p.Ala687Thr
NC_000009.11:g.134398374G>A
NM_007171.3:c.2125G>A
NR_148391.2:n.2093G>A
NR_148392.2:n.2311G>A
NR_148393.2:n.2232G>A
NR_148394.2:n.1986G>A
NR_148395.2:n.2384G>A
NR_148396.2:n.2018G>A
NR_148397.2:n.2143G>A
NR_148398.2:n.2098G>A
NR_148399.2:n.2624G>A
NR_148400.2:n.2223G>A

Protein change:

A535T

Links:

dbSNP: rs535544133

NCBI 1000 Genomes Browser:

rs535544133

Molecular consequence:

NM_001077365.2:c.2059G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001077366.2:c.1897G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001136113.2:c.2059G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001136114.2:c.1708G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353193.2:c.2125G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353194.2:c.1897G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353195.2:c.1708G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353196.2:c.1969G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353197.2:c.1963G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353198.2:c.1963G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353199.2:c.1774G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353200.2:c.1603G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374689.1:c.2047G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374690.1:c.1840G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374691.1:c.1708G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374692.1:c.1708G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374693.1:c.1708G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374695.1:c.1669G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_007171.4:c.2125G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_148391.2:n.2093G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148392.2:n.2311G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148393.2:n.2232G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148394.2:n.1986G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148395.2:n.2384G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148396.2:n.2018G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148397.2:n.2143G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148398.2:n.2098G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148399.2:n.2624G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148400.2:n.2223G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Autosomal recessive limb-girdle muscular dystrophy type 2K
Synonyms:: MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 1; MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 2K; Limb-girdle muscular dystrophy-dystroglycanopathy, type C1
Identifiers:: MONDO: MONDO:0012248; MedGen: C1836373; Orphanet: 86812; OMIM: 609308

Name:: Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1 (MDDGA1)
Synonyms:: Hydrocephalus, agyria and retinal dysplasia; Hard +/- E syndrome; Warburg syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009364; MedGen: C4284790; Orphanet: 588; Orphanet: 899; OMIM: 236670

Name:: Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1 (MDDGB1)
Synonyms:: MUSCULAR DYSTROPHY, CONGENITAL, POMT1-RELATED; MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH IMPAIRED INTELLECTUAL DEVELOPMENT), TYPE B, 1
Identifiers:: MONDO: MONDO:0013159; MedGen: C5436962; OMIM: 613155

Recent activity

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Cymbula granatina mitochondrial gene for 16S ribosomal RNA, partial sequence, ha...
Cymbula granatina mitochondrial gene for 16S ribosomal RNA, partial sequence, haplotype: CCMCg6
gi|1109514656|dbj|LC081289.1|

Nucleotide
Wilms tumor protein isoform A [Homo sapiens]
Wilms tumor protein isoform A [Homo sapiens]
gi|1327848674|ref|NP_000369.4|

Protein
PREDICTED: Moschus berezovskii neurofibromin 1 (NF1), transcript variant X3, mRN...
PREDICTED: Moschus berezovskii neurofibromin 1 (NF1), transcript variant X3, mRNA
gi|2492277260|ref|XM_055401457.1|

Nucleotide
Cymbula granatina mitochondrial gene for 12S ribosomal RNA, partial sequence, is...
Cymbula granatina mitochondrial gene for 12S ribosomal RNA, partial sequence, isolate: PTN Cg6
gi|921142743|dbj|LC074931.1|

Nucleotide
JGI_CAAJ544.rev NIH_XGC_tropBrn2 Xenopus tropicalis cDNA clone IMAGE:7640705 3',...
JGI_CAAJ544.rev NIH_XGC_tropBrn2 Xenopus tropicalis cDNA clone IMAGE:7640705 3', mRNA sequence
gi|71458030|gnl|dbEST|30351338|gb|C 31.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000895953	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 31, 2018)	unknown	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

SCV000895953

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Oct 31, 2018)

unknown

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	unknown	unknown	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

PMC

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.

Genetics in medicine : official journal of the American College of Medical Genetics. 2015 Mar 5; 17(5): 405-424

PMC [article]

PMCID:: PMC4544753
PMID:: 25741868
DOI:: 10.1038/gim.2015.30

Details of each submission

From Fulgent Genetics, Fulgent Genetics, SCV000895953.1

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

Last Updated: Sep 29, 2024

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