NM_001077365.2(POMT1):c.1414G>A (p.Val472Ile) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 30, 2021
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:: RCV001929572.4

Allele description [Variation Report for NM_001077365.2(POMT1):c.1414G>A (p.Val472Ile)]

NM_001077365.2(POMT1):c.1414G>A (p.Val472Ile)

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.1414G>A (p.Val472Ile)

HGVS:

NC_000009.12:g.131518885G>A
NG_008896.2:g.20984G>A
NM_001077365.2:c.1414G>AMANE SELECT
NM_001077366.2:c.1252G>A
NM_001136113.2:c.1414G>A
NM_001136114.2:c.1063G>A
NM_001353193.2:c.1480G>A
NM_001353194.2:c.1252G>A
NM_001353195.2:c.1063G>A
NM_001353196.2:c.1324G>A
NM_001353197.2:c.1318G>A
NM_001353198.2:c.1318G>A
NM_001353199.2:c.1129G>A
NM_001353200.2:c.958G>A
NM_001374689.1:c.1402G>A
NM_001374690.1:c.1365+348G>A
NM_001374691.1:c.1063G>A
NM_001374692.1:c.1063G>A
NM_001374693.1:c.1063G>A
NM_001374695.1:c.1024G>A
NM_007171.3:c.1480G>A
NM_007171.4:c.1480G>A
NP_001070833.1:p.Val472Ile
NP_001070834.1:p.Val418Ile
NP_001129585.1:p.Val472Ile
NP_001129586.1:p.Val355Ile
NP_001340122.2:p.Val494Ile
NP_001340123.1:p.Val418Ile
NP_001340124.1:p.Val355Ile
NP_001340125.1:p.Val442Ile
NP_001340126.2:p.Val440Ile
NP_001340127.2:p.Val440Ile
NP_001340128.2:p.Val377Ile
NP_001340129.1:p.Val320Ile
NP_001361618.1:p.Val468Ile
NP_001361620.1:p.Val355Ile
NP_001361621.1:p.Val355Ile
NP_001361622.1:p.Val355Ile
NP_001361624.1:p.Val342Ile
NP_009102.4:p.Val494Ile
LRG_842t1:c.1480G>A
LRG_842t2:c.1414G>A
LRG_842:g.20984G>A
LRG_842p1:p.Val494Ile
LRG_842p2:p.Val472Ile
NC_000009.11:g.134394272G>A
NG_008896.1:g.20984G>A
NR_148391.2:n.1448G>A
NR_148392.2:n.1666G>A
NR_148393.2:n.1587G>A
NR_148394.2:n.1341G>A
NR_148395.2:n.1739G>A
NR_148396.2:n.1373G>A
NR_148397.2:n.1498G>A
NR_148398.2:n.1453G>A
NR_148399.2:n.1979G>A
NR_148400.2:n.1578G>A

Protein change:

V320I

Links:

dbSNP: rs943420374

NCBI 1000 Genomes Browser:

rs943420374

Molecular consequence:

NM_001374690.1:c.1365+348G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001077365.2:c.1414G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001077366.2:c.1252G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001136113.2:c.1414G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001136114.2:c.1063G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353193.2:c.1480G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353194.2:c.1252G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353195.2:c.1063G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353196.2:c.1324G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353197.2:c.1318G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353198.2:c.1318G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353199.2:c.1129G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353200.2:c.958G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374689.1:c.1402G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374691.1:c.1063G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374692.1:c.1063G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374693.1:c.1063G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374695.1:c.1024G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_007171.4:c.1480G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_148391.2:n.1448G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148392.2:n.1666G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148393.2:n.1587G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148394.2:n.1341G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148395.2:n.1739G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148396.2:n.1373G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148397.2:n.1498G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148398.2:n.1453G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148399.2:n.1979G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148400.2:n.1578G>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 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002201997	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 30, 2021)	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

SCV002201997

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 30, 2021)

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 Invitae, SCV002201997.2

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

Description

This sequence change replaces valine with isoleucine at codon 494 of the POMT1 protein (p.Val494Ile). The valine residue is highly conserved and there is a small physicochemical difference between valine and isoleucine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with POMT1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C25". The isoleucine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.

#	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: May 7, 2024

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