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NM_002979.5(SCP2):c.825+1G>T AND SCP2-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 24, 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:
RCV003409851.4

Allele description [Variation Report for NM_002979.5(SCP2):c.825+1G>T]

NM_002979.5(SCP2):c.825+1G>T

Gene:
SCP2:sterol carrier protein 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p32.3
Genomic location:
Preferred name:
NM_002979.5(SCP2):c.825+1G>T
HGVS:
  • NC_000001.11:g.52978368G>T
  • NG_012211.1:g.56093G>T
  • NM_001007098.3:c.693+1G>T
  • NM_001193599.2:c.753+1G>T
  • NM_001193600.2:c.693+1G>T
  • NM_001193617.2:c.582+1G>T
  • NM_001330587.2:c.825+1G>T
  • NM_002979.4:c.825+1G>T
  • NM_002979.5:c.825+1G>TMANE SELECT
  • NC_000001.10:g.53444040G>T
Links:
dbSNP: rs144132787
NCBI 1000 Genomes Browser:
rs144132787
Molecular consequence:
  • NM_001007098.3:c.693+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001193599.2:c.753+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001193600.2:c.693+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001193617.2:c.582+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001330587.2:c.825+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_002979.5:c.825+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
SCP2-related disorder
Synonyms:
SCP2-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004114359PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Aug 24, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 PreventionGenetics, part of Exact Sciences, SCV004114359.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The SCP2 c.825+1G>T variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant was reported in the homozygous state in an individual with adolescent onset dystonia (Table S2 - Zech et al. 2020. PubMed ID: 33098801). This variant is reported in 0.020% of alleles in individuals of European (Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-53444040-G-T). Variants that disrupt the consensus splice donor site in SCP2 are expected to be pathogenic. This variant is interpreted as likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024