NM_001077365.2(POMT1):c.2096A>G (p.Tyr699Cys) AND multiple conditions

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 27, 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:: RCV001966637.4

Allele description

NM_001077365.2(POMT1):c.2096A>G (p.Tyr699Cys)

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.2096A>G (p.Tyr699Cys)

HGVS:

NC_000009.12:g.131523024A>G
NG_008896.2:g.25123A>G
NM_001077365.2:c.2096A>GMANE SELECT
NM_001077366.2:c.1934A>G
NM_001136113.2:c.2096A>G
NM_001136114.2:c.1745A>G
NM_001353193.2:c.2162A>G
NM_001353194.2:c.1934A>G
NM_001353195.2:c.1745A>G
NM_001353196.2:c.2006A>G
NM_001353197.2:c.2000A>G
NM_001353198.2:c.2000A>G
NM_001353199.2:c.1811A>G
NM_001353200.2:c.1640A>G
NM_001374689.1:c.2084A>G
NM_001374690.1:c.1877A>G
NM_001374691.1:c.1745A>G
NM_001374692.1:c.1745A>G
NM_001374693.1:c.1745A>G
NM_001374695.1:c.1706A>G
NM_007171.4:c.2162A>G
NP_001070833.1:p.Tyr699Cys
NP_001070834.1:p.Tyr645Cys
NP_001129585.1:p.Tyr699Cys
NP_001129586.1:p.Tyr582Cys
NP_001340122.2:p.Tyr721Cys
NP_001340123.1:p.Tyr645Cys
NP_001340124.1:p.Tyr582Cys
NP_001340125.1:p.Tyr669Cys
NP_001340126.2:p.Tyr667Cys
NP_001340127.2:p.Tyr667Cys
NP_001340128.2:p.Tyr604Cys
NP_001340129.1:p.Tyr547Cys
NP_001361618.1:p.Tyr695Cys
NP_001361619.1:p.Tyr626Cys
NP_001361620.1:p.Tyr582Cys
NP_001361621.1:p.Tyr582Cys
NP_001361622.1:p.Tyr582Cys
NP_001361624.1:p.Tyr569Cys
NP_009102.4:p.Tyr721Cys
LRG_842t1:c.2162A>G
LRG_842t2:c.2096A>G
LRG_842:g.25123A>G
LRG_842p1:p.Tyr721Cys
LRG_842p2:p.Tyr699Cys
NC_000009.11:g.134398411A>G
NG_008896.1:g.25123A>G
NM_007171.3:c.2162A>G
NR_148391.2:n.2130A>G
NR_148392.2:n.2348A>G
NR_148393.2:n.2269A>G
NR_148394.2:n.2023A>G
NR_148395.2:n.2421A>G
NR_148396.2:n.2055A>G
NR_148397.2:n.2180A>G
NR_148398.2:n.2135A>G
NR_148399.2:n.2661A>G
NR_148400.2:n.2260A>G

Protein change:

Y547C

Links:

dbSNP: rs754444374

NCBI 1000 Genomes Browser:

rs754444374

Molecular consequence:

NM_001077365.2:c.2096A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001077366.2:c.1934A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001136113.2:c.2096A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001136114.2:c.1745A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353193.2:c.2162A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353194.2:c.1934A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353195.2:c.1745A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353196.2:c.2006A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353197.2:c.2000A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353198.2:c.2000A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353199.2:c.1811A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353200.2:c.1640A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374689.1:c.2084A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374690.1:c.1877A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374691.1:c.1745A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374692.1:c.1745A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374693.1:c.1745A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374695.1:c.1706A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_007171.4:c.2162A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_148391.2:n.2130A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148392.2:n.2348A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148393.2:n.2269A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148394.2:n.2023A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148395.2:n.2421A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148396.2:n.2055A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148397.2:n.2180A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148398.2:n.2135A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148399.2:n.2661A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148400.2:n.2260A>G - 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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gi|1350086282|gb|PTWH01000014.1||gn :PTWH01|N59559F_S17_L001_R1_001_contig_14

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002253499	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 27, 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

SCV002253499

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 27, 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 Invitae, SCV002253499.2

#	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 tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 721 of the POMT1 protein (p.Tyr721Cys). This variant is present in population databases (rs754444374, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with POMT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1471141). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on POMT1 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: Mar 30, 2024

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Relating variation to medicine