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NM_003640.5(ELP1):c.3161-2A>G AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Oct 9, 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:
RCV002030967.6

Allele description [Variation Report for NM_003640.5(ELP1):c.3161-2A>G]

NM_003640.5(ELP1):c.3161-2A>G

Gene:
ELP1:elongator acetyltransferase complex subunit 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q31.3
Genomic location:
Preferred name:
NM_003640.5(ELP1):c.3161-2A>G
HGVS:
  • NC_000009.12:g.108889395T>C
  • NG_008788.1:g.49934A>G
  • NM_001318360.2:c.2819-2A>G
  • NM_001330749.2:c.2114-2A>G
  • NM_003640.5:c.3161-2A>GMANE SELECT
  • LRG_251:g.49934A>G
  • NC_000009.11:g.111651675T>C
Links:
dbSNP: rs749548287
NCBI 1000 Genomes Browser:
rs749548287
Molecular consequence:
  • NM_001318360.2:c.2819-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001330749.2:c.2114-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_003640.5:c.3161-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002310396Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Oct 9, 2022) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

IKAP localizes to membrane ruffles with filamin A and regulates actin cytoskeleton organization and cell migration.

Johansen LD, Naumanen T, Knudsen A, Westerlund N, Gromova I, Junttila M, Nielsen C, Bøttzauw T, Tolkovsky A, Westermarck J, Coffey ET, Jäättelä M, Kallunki T.

J Cell Sci. 2008 Mar 15;121(Pt 6):854-64. doi: 10.1242/jcs.013722. Epub 2008 Feb 26.

PubMed [citation]
PMID:
18303054
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002310396.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 1520850). This variant has not been reported in the literature in individuals affected with ELP1-related conditions. This variant is present in population databases (rs749548287, gnomAD 0.002%). This sequence change affects an acceptor splice site in intron 28 of the ELP1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ELP1 are known to be pathogenic (PMID: 18303054, 24173031).

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

Last Updated: Sep 29, 2024