NM_001077365.2(POMT1):c.1469A>C (p.Glu490Ala) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 8, 2022
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:: RCV002042509.6

Allele description [Variation Report for NM_001077365.2(POMT1):c.1469A>C (p.Glu490Ala)]

NM_001077365.2(POMT1):c.1469A>C (p.Glu490Ala)

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.1469A>C (p.Glu490Ala)

HGVS:

NC_000009.12:g.131518940A>C
NG_008896.2:g.21039A>C
NM_001077365.2:c.1469A>CMANE SELECT
NM_001077366.2:c.1307A>C
NM_001136113.2:c.1469A>C
NM_001136114.2:c.1118A>C
NM_001353193.2:c.1535A>C
NM_001353194.2:c.1307A>C
NM_001353195.2:c.1118A>C
NM_001353196.2:c.1379A>C
NM_001353197.2:c.1373A>C
NM_001353198.2:c.1373A>C
NM_001353199.2:c.1184A>C
NM_001353200.2:c.1013A>C
NM_001374689.1:c.1457A>C
NM_001374690.1:c.1365+403A>C
NM_001374691.1:c.1118A>C
NM_001374692.1:c.1118A>C
NM_001374693.1:c.1118A>C
NM_001374695.1:c.1079A>C
NM_007171.4:c.1535A>C
NP_001070833.1:p.Glu490Ala
NP_001070834.1:p.Glu436Ala
NP_001129585.1:p.Glu490Ala
NP_001129586.1:p.Glu373Ala
NP_001340122.2:p.Glu512Ala
NP_001340123.1:p.Glu436Ala
NP_001340124.1:p.Glu373Ala
NP_001340125.1:p.Glu460Ala
NP_001340126.2:p.Glu458Ala
NP_001340127.2:p.Glu458Ala
NP_001340128.2:p.Glu395Ala
NP_001340129.1:p.Glu338Ala
NP_001361618.1:p.Glu486Ala
NP_001361620.1:p.Glu373Ala
NP_001361621.1:p.Glu373Ala
NP_001361622.1:p.Glu373Ala
NP_001361624.1:p.Glu360Ala
NP_009102.4:p.Glu512Ala
LRG_842t1:c.1535A>C
LRG_842t2:c.1469A>C
LRG_842:g.21039A>C
LRG_842p1:p.Glu512Ala
LRG_842p2:p.Glu490Ala
NC_000009.11:g.134394327A>C
NG_008896.1:g.21039A>C
NR_148391.2:n.1503A>C
NR_148392.2:n.1721A>C
NR_148393.2:n.1642A>C
NR_148394.2:n.1396A>C
NR_148395.2:n.1794A>C
NR_148396.2:n.1428A>C
NR_148397.2:n.1553A>C
NR_148398.2:n.1508A>C
NR_148399.2:n.2034A>C
NR_148400.2:n.1633A>C

Protein change:

E338A

Links:

dbSNP: rs2131857011

NCBI 1000 Genomes Browser:

rs2131857011

Molecular consequence:

NM_001374690.1:c.1365+403A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001077365.2:c.1469A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001077366.2:c.1307A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001136113.2:c.1469A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001136114.2:c.1118A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353193.2:c.1535A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353194.2:c.1307A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353195.2:c.1118A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353196.2:c.1379A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353197.2:c.1373A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353198.2:c.1373A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353199.2:c.1184A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353200.2:c.1013A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374689.1:c.1457A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374691.1:c.1118A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374692.1:c.1118A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374693.1:c.1118A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374695.1:c.1079A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_007171.4:c.1535A>C - missense variant - [Sequence Ontology: SO:0001583]
NR_148391.2:n.1503A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148392.2:n.1721A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148393.2:n.1642A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148394.2:n.1396A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148395.2:n.1794A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148396.2:n.1428A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148397.2:n.1553A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148398.2:n.1508A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148399.2:n.2034A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148400.2:n.1633A>C - 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 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

Name:: Walker-Warburg congenital muscular dystrophy
Synonyms:: Muscular dystrophy-dystroglycanopathy, type A; Walker-Warburg syndrome
Identifiers:: MONDO: MONDO:0000171; MedGen: C0265221; Orphanet: 899; OMIM: PS236670

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Taxonomy
SLC47A2 solute carrier family 47 member 2 [Homo sapiens]
SLC47A2 solute carrier family 47 member 2 [Homo sapiens]
Gene ID:146802

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002296044	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 8, 2022)	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

SCV002296044

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 8, 2022)

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002296044.3

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. This variant has not been reported in the literature in individuals affected with POMT1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glutamic acid, which is acidic and polar, with alanine, which is neutral and non-polar, at codon 512 of the POMT1 protein (p.Glu512Ala).

#	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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