NM_017739.4(POMGNT1):c.1510G>A (p.Val504Ile) AND not specified

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Apr 24, 2019
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:: RCV000267239.11

Allele description [Variation Report for NM_017739.4(POMGNT1):c.1510G>A (p.Val504Ile)]

NM_017739.4(POMGNT1):c.1510G>A (p.Val504Ile)

Genes:

POMGNT1:protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-) [Gene - OMIM - HGNC]
TSPAN1:tetraspanin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p34.1

Genomic location:

Preferred name:

NM_017739.4(POMGNT1):c.1510G>A (p.Val504Ile)

HGVS:

NC_000001.11:g.46192127C>T
NG_009205.3:g.33179G>A
NM_001243766.2:c.1510G>A
NM_001290129.2:c.1444G>A
NM_001290130.2:c.1081G>A
NM_017739.4:c.1510G>AMANE SELECT
NP_001230695.2:p.Val504Ile
NP_001277058.2:p.Val482Ile
NP_001277059.2:p.Val361Ile
NP_060209.3:p.Val504Ile
NP_060209.4:p.Val504Ile
LRG_701t1:c.1510G>A
LRG_701t2:c.1510G>A
LRG_701:g.33179G>A
LRG_701p1:p.Val504Ile
LRG_701p2:p.Val504Ile
NC_000001.10:g.46657799C>T
NG_009205.2:g.33179G>A
NM_017739.3:c.1510G>A
Q8WZA1:p.Val504Ile

Protein change:

V361I

Links:

UniProtKB: Q8WZA1#VAR_030646; dbSNP: rs17102066

NCBI 1000 Genomes Browser:

rs17102066

Molecular consequence:

NM_001243766.2:c.1510G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001290129.2:c.1444G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001290130.2:c.1081G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_017739.4:c.1510G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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dif-1 Protein dif-1 [Caenorhabditis elegans]
dif-1 Protein dif-1 [Caenorhabditis elegans]
Gene ID:177530

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000331162	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Benign (Jan 12, 2016)	germline	clinical testing	Citation Link,
SCV000596515	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Apr 24, 2019)	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

SCV000331162

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Benign
(Jan 12, 2016)

germline

clinical testing

Citation Link,

SCV000596515

Genetic Services Laboratory, University of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Apr 24, 2019)

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	3	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Eurofins Ntd Llc (ga), SCV000331162.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	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		3	not provided	not provided	not provided

From Genetic Services Laboratory, University of Chicago, SCV000596515.2

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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