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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Arabidopsis thaliana cytochrome p450 71b6 (CYP71B6), mRNA
Arabidopsis thaliana cytochrome p450 71b6 (CYP71B6), mRNA
gi|1063701233|ref|NM_127979.3|

Nucleotide
B.taurus CI-AGGG mRNA for ubiquinone oxidoreductase complex
B.taurus CI-AGGG mRNA for ubiquinone oxidoreductase complex
gi|231|emb|X63216.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000621701	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Oct 11, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000621701

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Oct 11, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000621701.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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