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NM_133433.4(NIPBL):c.2T>A (p.Met1Lys) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 5, 2024
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:
RCV004700178.1

Allele description [Variation Report for NM_133433.4(NIPBL):c.2T>A (p.Met1Lys)]

NM_133433.4(NIPBL):c.2T>A (p.Met1Lys)

Gene:
NIPBL:NIPBL cohesin loading factor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5p13.2
Genomic location:
Preferred name:
NM_133433.4(NIPBL):c.2T>A (p.Met1Lys)
HGVS:
  • NC_000005.10:g.36953698T>A
  • NG_006987.2:g.81816T>A
  • NM_015384.5:c.2T>A
  • NM_133433.4:c.2T>AMANE SELECT
  • NP_056199.2:p.Met1Lys
  • NP_597677.2:p.Met1Lys
  • NC_000005.9:g.36953800T>A
  • NG_006987.1:g.81816T>A
  • NM_133433.3:c.2T>A
Protein change:
M1K; MET1LYS
Links:
OMIM: 608667.0001; dbSNP: rs121918264
NCBI 1000 Genomes Browser:
rs121918264
Molecular consequence:
  • NM_015384.5:c.2T>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_133433.4:c.2T>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_015384.5:c.2T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_133433.4:c.2T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV005201794GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Pathogenic
(Feb 5, 2024)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV005201794.1

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

Description

Initiation codon variant in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 26147798, 22581668, 24038889, 15146186)

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

Last Updated: Sep 29, 2024