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NM_002299.4(LCT):c.4866+2T>G AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 1, 2023
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:
RCV003669389.2

Allele description [Variation Report for NM_002299.4(LCT):c.4866+2T>G]

NM_002299.4(LCT):c.4866+2T>G

Gene:
LCT:lactase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q21.3
Genomic location:
Preferred name:
NM_002299.4(LCT):c.4866+2T>G
HGVS:
  • NC_000002.12:g.135800605A>C
  • NG_008104.2:g.59565T>G
  • NM_002299.4:c.4866+2T>GMANE SELECT
  • LRG_338:g.59565T>G
  • NC_000002.11:g.136558175A>C
  • NM_002299.3:c.4866+2T>G
Molecular consequence:
  • NM_002299.4:c.4866+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]

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
SCV004389763Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Mar 1, 2023) 		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

Mutations in the translated region of the lactase gene (LCT) underlie congenital lactase deficiency.

Kuokkanen M, Kokkonen J, Enattah NS, Ylisaukko-Oja T, Komu H, Varilo T, Peltonen L, Savilahti E, Jarvela I.

Am J Hum Genet. 2006 Feb;78(2):339-44. Epub 2005 Dec 15.

PubMed [citation]
PMID:
16400612
PMCID:
PMC1380240
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004389763.1

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

Description

This sequence change affects a donor splice site in intron 12 of the LCT 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 LCT are known to be pathogenic (PMID: 16400612, 25881162). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with LCT-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.

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

Last Updated: Sep 29, 2024