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NM_000020.3(ACVRL1):c.313_313+1del AND Cardiovascular phenotype

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
May 18, 2020
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:
RCV002320586.2

Allele description [Variation Report for NM_000020.3(ACVRL1):c.313_313+1del]

NM_000020.3(ACVRL1):c.313_313+1del

Gene:
ACVRL1:activin A receptor like type 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
12q13.13
Genomic location:
Preferred name:
NM_000020.3(ACVRL1):c.313_313+1del
HGVS:
  • NC_000012.12:g.51913350_51913351del
  • NG_009549.1:g.10933_10934del
  • NM_000020.3:c.313_313+1delMANE SELECT
  • NM_001077401.2:c.313_313+1del
  • LRG_543t1:c.313_313+1del
  • LRG_543:g.10933_10934del
  • NC_000012.11:g.52307134_52307135del
  • NM_000020.2:c.313_313+1delGG
Molecular consequence:
  • NM_000020.3:c.313_313+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001077401.2:c.313_313+1del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Cardiovascular phenotype
Identifiers:
MedGen: CN230736

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002607709Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(May 18, 2020) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Ambry Genetics, SCV002607709.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.313_313+1delGG variant results from a deletion of two nucleotides at positions c.313 and c.313+1 and involves the canonical splice donor site after coding exon 2 of the ACVRL1 gene. The canonical splice donor site is highly conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, the native donor splice site is shifted two nucleotides upstream resulting in a translational frameshift with a predicted alternate stop codon; however, direct evidence is unavailable. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as likely pathogenic.

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

Last Updated: May 1, 2024