NM_001077365.2(POMT1):c.1457G>A (p.Trp486Ter) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 10, 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:: RCV001205242.6

Allele description [Variation Report for NM_001077365.2(POMT1):c.1457G>A (p.Trp486Ter)]

NM_001077365.2(POMT1):c.1457G>A (p.Trp486Ter)

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.1457G>A (p.Trp486Ter)

HGVS:

NC_000009.12:g.131518928G>A
NG_008896.1:g.21027G>A
NM_001077365.2:c.1457G>AMANE SELECT
NM_001077366.2:c.1295G>A
NM_001136113.2:c.1457G>A
NM_001136114.2:c.1106G>A
NM_001353193.2:c.1523G>A
NM_001353194.2:c.1295G>A
NM_001353195.2:c.1106G>A
NM_001353196.2:c.1367G>A
NM_001353197.2:c.1361G>A
NM_001353198.2:c.1361G>A
NM_001353199.2:c.1172G>A
NM_001353200.2:c.1001G>A
NM_001374689.1:c.1445G>A
NM_001374690.1:c.1365+391G>A
NM_001374691.1:c.1106G>A
NM_001374692.1:c.1106G>A
NM_001374693.1:c.1106G>A
NM_001374695.1:c.1067G>A
NM_007171.4:c.1523G>A
NP_001070833.1:p.Trp486Ter
NP_001070834.1:p.Trp432Ter
NP_001129585.1:p.Trp486Ter
NP_001129586.1:p.Trp369Ter
NP_001340122.2:p.Trp508Ter
NP_001340123.1:p.Trp432Ter
NP_001340124.1:p.Trp369Ter
NP_001340125.1:p.Trp456Ter
NP_001340126.2:p.Trp454Ter
NP_001340127.2:p.Trp454Ter
NP_001340128.2:p.Trp391Ter
NP_001340129.1:p.Trp334Ter
NP_001361618.1:p.Trp482Ter
NP_001361620.1:p.Trp369Ter
NP_001361621.1:p.Trp369Ter
NP_001361622.1:p.Trp369Ter
NP_001361624.1:p.Trp356Ter
NP_009102.4:p.Trp508Ter
LRG_842t1:c.1523G>A
LRG_842t2:c.1457G>A
LRG_842p1:p.Trp508Ter
LRG_842p2:p.Trp486Ter
NC_000009.11:g.134394315G>A
NM_007171.3:c.1523G>A
NR_148391.2:n.1491G>A
NR_148392.2:n.1709G>A
NR_148393.2:n.1630G>A
NR_148394.2:n.1384G>A
NR_148395.2:n.1782G>A
NR_148396.2:n.1416G>A
NR_148397.2:n.1541G>A
NR_148398.2:n.1496G>A
NR_148399.2:n.2022G>A
NR_148400.2:n.1621G>A

Protein change:

W334*

Links:

dbSNP: rs1191391104

NCBI 1000 Genomes Browser:

rs1191391104

Molecular consequence:

NM_001374690.1:c.1365+391G>A - intron variant - [Sequence Ontology: SO:0001627]
NR_148391.2:n.1491G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148392.2:n.1709G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148393.2:n.1630G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148394.2:n.1384G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148395.2:n.1782G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148396.2:n.1416G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148397.2:n.1541G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148398.2:n.1496G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148399.2:n.2022G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148400.2:n.1621G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001077365.2:c.1457G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001077366.2:c.1295G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001136113.2:c.1457G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001136114.2:c.1106G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353193.2:c.1523G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353194.2:c.1295G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353195.2:c.1106G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353196.2:c.1367G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353197.2:c.1361G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353198.2:c.1361G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353199.2:c.1172G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353200.2:c.1001G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374689.1:c.1445G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374691.1:c.1106G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374692.1:c.1106G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374693.1:c.1106G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374695.1:c.1067G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_007171.4:c.1523G>A - nonsense - [Sequence Ontology: SO:0001587]

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
SCV001376483	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 10, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 12369018, 15637732, 16575835, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001376483

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 10, 2022)

germline

clinical testing

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

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

Mutations in the O-mannosyltransferase gene POMT1 give rise to the severe neuronal migration disorder Walker-Warburg syndrome.

Beltrán-Valero de Bernabé D, Currier S, Steinbrecher A, Celli J, van Beusekom E, van der Zwaag B, Kayserili H, Merlini L, Chitayat D, Dobyns WB, Cormand B, Lehesjoki AE, Cruces J, Voit T, Walsh CA, van Bokhoven H, Brunner HG.

Am J Hum Genet. 2002 Nov;71(5):1033-43. Epub 2002 Oct 4.

PubMed [citation]

PMID:: 12369018
PMCID:: PMC419999

Mutations in POMT1 are found in a minority of patients with Walker-Warburg syndrome.

Currier SC, Lee CK, Chang BS, Bodell AL, Pai GS, Job L, Lagae LG, Al-Gazali LI, Eyaid WM, Enns G, Dobyns WB, Walsh CA.

Am J Med Genet A. 2005 Feb 15;133A(1):53-7.

PubMed [citation]

PMID:: 15637732

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001376483.5

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

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 936444). 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 creates a premature translational stop signal (p.Trp508*) in the POMT1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in POMT1 are known to be pathogenic (PMID: 12369018, 15637732, 16575835).

#	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

ClinVar

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