NM_001077365.2(POMT1):c.174CTT[2] (p.Phe60del) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 30, 2024
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:: RCV001205238.7

Allele description [Variation Report for NM_001077365.2(POMT1):c.174CTT[2] (p.Phe60del)]

NM_001077365.2(POMT1):c.174CTT[2] (p.Phe60del)

Gene:

POMT1:protein O-mannosyltransferase 1 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

9q34.13

Genomic location:

Preferred name:

NM_001077365.2(POMT1):c.174CTT[2] (p.Phe60del)

HGVS:

NC_000009.12:g.131506164_131506166TCT[2]
NC_000009.12:g.131506165CTT[2]
NG_008896.2:g.8264CTT[2]
NM_001077365.2:c.174CTT[2]MANE SELECT
NM_001077366.2:c.12CTT[2]
NM_001136113.2:c.174CTT[2]
NM_001136114.1:c.-122-239TCT[2]
NM_001136114.2:c.-122-239TCT[2]
NM_001353193.2:c.174CTT[2]
NM_001353194.2:c.12CTT[2]
NM_001353195.2:c.-122-239TCT[2]
NM_001353196.2:c.123-239TCT[2]
NM_001353197.2:c.12CTT[2]
NM_001353198.2:c.12CTT[2]
NM_001353199.2:c.-122-239TCT[2]
NM_001353200.2:c.-80-239TCT[2]
NM_001374689.1:c.12CTT[2]
NM_001374690.1:c.174CTT[2]
NM_001374691.1:c.-71-1204TCT[2]
NM_001374692.1:c.-71-1204TCT[2]
NM_001374693.1:c.12CTT[2]
NM_001374695.1:c.-30+1824TCT[2]
NM_007171.4:c.174CTT[2]
NP_001070833.1:p.Phe60del
NP_001070833.1:p.Phe60del
NP_001070834.1:p.Phe6del
NP_001129585.1:p.Phe60del
NP_001340122.2:p.Phe60del
NP_001340123.1:p.Phe6del
NP_001340126.2:p.Phe6del
NP_001340127.2:p.Phe6del
NP_001361618.1:p.Phe6del
NP_001361619.1:p.Phe60del
NP_001361622.1:p.Phe6del
NP_009102.4:p.Phe60del
LRG_842t1:c.174CTT[2]
LRG_842t2:c.174CTT[2]
LRG_842:g.8264CTT[2]
LRG_842p1:p.Phe60del
LRG_842p2:p.Phe60del
NC_000009.11:g.134381551_134381553del
NC_000009.11:g.134381552CTT[2]
NG_008896.1:g.8264CTT[2]
NM_001077365.2:c.174_176CTT[2]MANE SELECT
NM_007171.3:c.173_175delTCT
NM_007171.3:c.180_182del
NM_007171.3:c.180_182delCTT
NM_007171.4:c.180_182del
NR_148391.2:n.208CTT[2]
NR_148392.2:n.360CTT[2]
NR_148393.2:n.208CTT[2]
NR_148394.2:n.208CTT[2]
NR_148395.2:n.360CTT[2]
NR_148398.2:n.208CTT[2]
NR_148399.2:n.600CTT[2]

Protein change:

F60del

Links:

dbSNP: rs750195040

NCBI 1000 Genomes Browser:

rs750195040

Molecular consequence:

NM_001077365.2:c.174CTT[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001077366.2:c.12CTT[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001136113.2:c.174CTT[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353193.2:c.174CTT[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353194.2:c.12CTT[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353197.2:c.12CTT[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353198.2:c.12CTT[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374689.1:c.12CTT[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374690.1:c.174CTT[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374693.1:c.12CTT[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_007171.4:c.174CTT[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001136114.2:c.-122-239TCT[2] - intron variant - [Sequence Ontology: SO:0001627]
NM_001353195.2:c.-122-239TCT[2] - intron variant - [Sequence Ontology: SO:0001627]
NM_001353196.2:c.123-239TCT[2] - intron variant - [Sequence Ontology: SO:0001627]
NM_001353199.2:c.-122-239TCT[2] - intron variant - [Sequence Ontology: SO:0001627]
NM_001353200.2:c.-80-239TCT[2] - intron variant - [Sequence Ontology: SO:0001627]
NM_001374691.1:c.-71-1204TCT[2] - intron variant - [Sequence Ontology: SO:0001627]
NM_001374692.1:c.-71-1204TCT[2] - intron variant - [Sequence Ontology: SO:0001627]
NM_001374695.1:c.-30+1824TCT[2] - intron variant - [Sequence Ontology: SO:0001627]
NR_148391.2:n.208CTT[2] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148392.2:n.360CTT[2] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148393.2:n.208CTT[2] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148394.2:n.208CTT[2] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148395.2:n.360CTT[2] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148398.2:n.208CTT[2] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148399.2:n.600CTT[2] - 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
SCV001376479	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 30, 2024)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 17559086, 22323514, 27193224, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001376479

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 30, 2024)

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

Molecular heterogeneity in fetal forms of type II lissencephaly.

Bouchet C, Gonzales M, Vuillaumier-Barrot S, Devisme L, Lebizec C, Alanio E, Bazin A, Bessières-Grattagliano B, Bigi N, Blanchet P, Bonneau D, Bonnières M, Carles D, Delahaye S, Fallet-Bianco C, Figarella-Branger D, Gaillard D, Gasser B, Guimiot F, Joubert M, Laurent N, Liprandi A, et al.

Hum Mutat. 2007 Oct;28(10):1020-7.

PubMed [citation]

PMID:: 17559086

Cobblestone lissencephaly: neuropathological subtypes and correlations with genes of dystroglycanopathies.

Devisme L, Bouchet C, Gonzalès M, Alanio E, Bazin A, Bessières B, Bigi N, Blanchet P, Bonneau D, Bonnières M, Bucourt M, Carles D, Clarisse B, Delahaye S, Fallet-Bianco C, Figarella-Branger D, Gaillard D, Gasser B, Delezoide AL, Guimiot F, Joubert M, Laurent N, et al.

Brain. 2012 Feb;135(Pt 2):469-82. doi: 10.1093/brain/awr357. Epub 2012 Feb 9.

PubMed [citation]

PMID:: 22323514

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001376479.5

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

Description

This variant, c.180_182del, results in the deletion of 1 amino acid(s) of the POMT1 protein (p.Phe60del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs750195040, gnomAD 0.006%). This variant has been observed in individual(s) with cobblestone lissencephaly and/or severe congenital muscular dystrophy (PMID: 17559086, 22323514, 27193224; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as c.178-180delTTC. ClinVar contains an entry for this variant (Variation ID: 431953). For these reasons, this variant has been classified as Pathogenic.

#	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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