NM_001077365.2(POMT1):c.1483G>A (p.Ala495Thr) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Sep 12, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000381543.5

Allele description [Variation Report for NM_001077365.2(POMT1):c.1483G>A (p.Ala495Thr)]

NM_001077365.2(POMT1):c.1483G>A (p.Ala495Thr)

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.1483G>A (p.Ala495Thr)

HGVS:

NC_000009.12:g.131518954G>A
NG_008896.1:g.21053G>A
NM_001077365.2:c.1483G>AMANE SELECT
NM_001077366.2:c.1321G>A
NM_001136113.2:c.1483G>A
NM_001136114.2:c.1132G>A
NM_001353193.2:c.1549G>A
NM_001353194.2:c.1321G>A
NM_001353195.2:c.1132G>A
NM_001353196.2:c.1393G>A
NM_001353197.2:c.1387G>A
NM_001353198.2:c.1387G>A
NM_001353199.2:c.1198G>A
NM_001353200.2:c.1027G>A
NM_001374689.1:c.1471G>A
NM_001374690.1:c.1365+417G>A
NM_001374691.1:c.1132G>A
NM_001374692.1:c.1132G>A
NM_001374693.1:c.1132G>A
NM_001374695.1:c.1093G>A
NM_007171.3:c.1549G>A
NM_007171.4:c.1549G>A
NP_001070833.1:p.Ala495Thr
NP_001070834.1:p.Ala441Thr
NP_001129585.1:p.Ala495Thr
NP_001129586.1:p.Ala378Thr
NP_001340122.2:p.Ala517Thr
NP_001340123.1:p.Ala441Thr
NP_001340124.1:p.Ala378Thr
NP_001340125.1:p.Ala465Thr
NP_001340126.2:p.Ala463Thr
NP_001340127.2:p.Ala463Thr
NP_001340128.2:p.Ala400Thr
NP_001340129.1:p.Ala343Thr
NP_001361618.1:p.Ala491Thr
NP_001361620.1:p.Ala378Thr
NP_001361621.1:p.Ala378Thr
NP_001361622.1:p.Ala378Thr
NP_001361624.1:p.Ala365Thr
NP_009102.4:p.Ala517Thr
LRG_842t1:c.1549G>A
LRG_842t2:c.1483G>A
LRG_842p1:p.Ala517Thr
LRG_842p2:p.Ala495Thr
NC_000009.11:g.134394341G>A
NR_148391.2:n.1517G>A
NR_148392.2:n.1735G>A
NR_148393.2:n.1656G>A
NR_148394.2:n.1410G>A
NR_148395.2:n.1808G>A
NR_148396.2:n.1442G>A
NR_148397.2:n.1567G>A
NR_148398.2:n.1522G>A
NR_148399.2:n.2048G>A
NR_148400.2:n.1647G>A

Protein change:

A343T

Links:

dbSNP: rs774039973

NCBI 1000 Genomes Browser:

rs774039973

Molecular consequence:

NM_001374690.1:c.1365+417G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001077365.2:c.1483G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001077366.2:c.1321G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001136113.2:c.1483G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001136114.2:c.1132G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353193.2:c.1549G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353194.2:c.1321G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353195.2:c.1132G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353196.2:c.1393G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353197.2:c.1387G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353198.2:c.1387G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353199.2:c.1198G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353200.2:c.1027G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374689.1:c.1471G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374691.1:c.1132G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374692.1:c.1132G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374693.1:c.1132G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374695.1:c.1093G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_007171.4:c.1549G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_148391.2:n.1517G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148392.2:n.1735G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148393.2:n.1656G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148394.2:n.1410G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148395.2:n.1808G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148396.2:n.1442G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148397.2:n.1567G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148398.2:n.1522G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148399.2:n.2048G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148400.2:n.1647G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000342548	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions)	Uncertain significance (Jun 3, 2016)	germline	clinical testing	Citation Link,
SCV003840704	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Sep 12, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000342548

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions)

Uncertain significance
(Jun 3, 2016)

germline

clinical testing

Citation Link,

SCV003840704

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Sep 12, 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
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000342548.4

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

#	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		1	not provided	not provided	not provided

From GeneDx, SCV003840704.1

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 30564623)

#	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: Apr 1, 2023

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