NM_001128159.3(VPS53):c.1557-30T>C AND Pontocerebellar hypoplasia type 2E

Germline classification:: Benign (1 submission)
Last evaluated:: Jul 14, 2021
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:: RCV001544171.2

Allele description [Variation Report for NM_001128159.3(VPS53):c.1557-30T>C]

NM_001128159.3(VPS53):c.1557-30T>C

Genes:

LOC126862456:CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:463241-464440 [Gene]
VPS53:VPS53 subunit of GARP complex [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p13.3

Genomic location:

Preferred name:

NM_001128159.3(VPS53):c.1557-30T>C

HGVS:

NC_000017.11:g.560603A>G
NG_034190.1:g.159254T>C
NM_001128159.3:c.1557-30T>CMANE SELECT
NM_001366253.2:c.1557-30T>C
NM_001366254.2:c.963-30T>C
NM_018289.4:c.1470-30T>C
NC_000017.10:g.463843A>G

Links:

dbSNP: rs741677

NCBI 1000 Genomes Browser:

rs741677

Molecular consequence:

NM_001128159.3:c.1557-30T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001366253.2:c.1557-30T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001366254.2:c.963-30T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_018289.4:c.1470-30T>C - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Pontocerebellar hypoplasia type 2E
Identifiers:: MONDO: MONDO:0014370; MedGen: C4014488; Orphanet: 247198; OMIM: 615851

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001763159	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jul 14, 2021)	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

SCV001763159

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Jul 14, 2021)

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	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 Genome-Nilou Lab, SCV001763159.1

#	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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