NM_001077365.2(POMT1):c.174CTT[2] (p.Phe60del) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 19, 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:: RCV000498358.4

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)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000589544	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jan 19, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000589544

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Jan 19, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000589544.5

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

Description

Published functional studies demonstrate a damaging effect (Yang et al., 2016); Not observed at significant frequency in large population cohorts (gnomAD); In-frame deletion of 1 amino acid in a non-repeat region; In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 17559086, 22323514, 31589614, 33200426, 27193224)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 30, 2024

ClinVar

Relating variation to medicine