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NM_206937.2(LIG4):c.2592_2595del (p.Ile864fs) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 11, 2017
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:
RCV000519485.1

Allele description [Variation Report for NM_206937.2(LIG4):c.2592_2595del (p.Ile864fs)]

NM_206937.2(LIG4):c.2592_2595del (p.Ile864fs)

Gene:
LIG4:DNA ligase 4 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
13q33.3
Genomic location:
Preferred name:
NM_206937.2(LIG4):c.2592_2595del (p.Ile864fs)
HGVS:
  • NC_000013.11:g.108208675_108208678del
  • NG_007396.1:g.11858_11861del
  • NM_001098268.2:c.2592_2595del
  • NM_001330595.2:c.2391_2394del
  • NM_001352598.2:c.2592_2595del
  • NM_001352599.2:c.2592_2595del
  • NM_001352600.2:c.2592_2595del
  • NM_001352601.2:c.2592_2595del
  • NM_001352602.2:c.2592_2595del
  • NM_001352603.1:c.2592_2595del
  • NM_001352604.2:c.2628_2631del
  • NM_001379095.1:c.2592_2595del
  • NM_002312.3:c.2592_2595del
  • NM_206937.2:c.2592_2595delMANE SELECT
  • NP_001091738.1:p.Ile864fs
  • NP_001317524.1:p.Ile797fs
  • NP_001339527.1:p.Ile864fs
  • NP_001339528.1:p.Ile864fs
  • NP_001339529.1:p.Ile864fs
  • NP_001339530.1:p.Ile864fs
  • NP_001339531.1:p.Ile864fs
  • NP_001339532.1:p.Ile864fs
  • NP_001339533.1:p.Ile876fs
  • NP_001366024.1:p.Ile864fs
  • NP_002303.2:p.Ile864fs
  • NP_996820.1:p.Ile864fs
  • LRG_79t1:c.2592_2595del
  • LRG_79:g.11858_11861del
  • LRG_79p1:p.Ile864fs
  • NC_000013.10:g.108861022_108861025del
  • NC_000013.10:g.108861023_108861026del
  • NM_002312.3:c.2592_2595delAATT
Protein change:
I797fs
Links:
dbSNP: rs765317127
NCBI 1000 Genomes Browser:
rs765317127
Molecular consequence:
  • NM_001098268.2:c.2592_2595del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001330595.2:c.2391_2394del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001352598.2:c.2592_2595del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001352599.2:c.2592_2595del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001352600.2:c.2592_2595del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001352601.2:c.2592_2595del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001352602.2:c.2592_2595del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001352603.1:c.2592_2595del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001352604.2:c.2628_2631del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001379095.1:c.2592_2595del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_002312.3:c.2592_2595del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_206937.2:c.2592_2595del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV000621701GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Oct 11, 2017) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000621701.2

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

Description

The c.2592_2595delAATT variant in the LIG4 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant causes a frameshift starting with codon Isoleucine 864, changes this amino acid to a Methionine residue, and creates a premature Stop codon at position 25 of the new reading frame, denoted p.Ile864MetfsX25. This variant is predicted to cause loss of normal protein function through protein truncation. The c.2592_2595delAATT variant is observed in 5/111,658 alleles (0.0045%) from individuals of non-Finnish European ancestry in the gnomAD dataset (Lek et al., 2016). We interpret c.2592_2595delAATT as a variant of uncertain significance.

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

Last Updated: Sep 29, 2024