rs772226399

chr13-108209993-CTCTTT-C

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong

The NM_206937.2(LIG4):c.1271_1275del(p.Lys424ArgfsTer20) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00022 in 1,612,524 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★).

Frequency

Genomes: 𝑓 0.00025 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00022 ( 0 hom. )

Consequence

LIG4
NM_206937.2 frameshift

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:10

Conservation

PhyloP100: 7.81

Variant links:

Genes affected

LIG4 (HGNC:6601): (DNA ligase 4) The protein encoded by this gene is a DNA ligase that joins single-strand breaks in a double-stranded polydeoxynucleotide in an ATP-dependent reaction. This protein is essential for V(D)J recombination and DNA double-strand break (DSB) repair through nonhomologous end joining (NHEJ). This protein forms a complex with the X-ray repair cross complementing protein 4 (XRCC4), and further interacts with the DNA-dependent protein kinase (DNA-PK). Both XRCC4 and DNA-PK are known to be required for NHEJ. The crystal structure of the complex formed by this protein and XRCC4 has been resolved. Defects in this gene are the cause of LIG4 syndrome. Alternatively spliced transcript variants encoding the same protein have been observed. [provided by RefSeq, Jul 2008]

LIG4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 ACMG points.

PVS1

Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 35 pathogenic variants in the truncated region.

PM2

Very rare variant in population databases, with high coverage;

PP5

Variant 13-108209993-CTCTTT-C is Pathogenic according to our data. Variant chr13-108209993-CTCTTT-C is described in ClinVar as [Pathogenic]. Clinvar id is 279838.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-108209993-CTCTTT-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LIG4	NM_206937.2 linkuse as main transcript	c.1271_1275del	p.Lys424ArgfsTer20	frameshift_variant	3/3	ENST00000442234.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LIG4	ENST00000442234.6 linkuse as main transcript	c.1271_1275del	p.Lys424ArgfsTer20	frameshift_variant	3/3	1	NM_206937.2	P1

Frequencies

GnomAD3 genomes

AF:

0.000250

AC:

AN:

152220

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000362

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000196

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000265

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.000156

AC:

AN:

250062

Hom.:

AF XY:

0.000155

AC XY:

AN XY:

135328

show subpopulations

Gnomad AFR exome

AF:

0.000246

Gnomad AMR exome

AF:

0.000116

Gnomad ASJ exome

AF:

0.0000992

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.000163

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000194

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000216

AC:

316

AN:

1460186

Hom.:

AF XY:

0.000202

AC XY:

147

AN XY:

726476

show subpopulations

Gnomad4 AFR exome

AF:

0.000388

Gnomad4 AMR exome

AF:

0.000179

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000302

Gnomad4 SAS exome

AF:

0.000128

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000233

Gnomad4 OTH exome

AF:

0.000215

GnomAD4 genome

AF:

0.000249

AC:

AN:

152338

Hom.:

Cov.:

AF XY:

0.000215

AC XY:

AN XY:

74514

show subpopulations

Gnomad4 AFR

AF:

0.000361

Gnomad4 AMR

AF:

0.000196

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000265

Gnomad4 OTH

AF:

0.000473

Alfa

AF:

0.000217

Hom.:

Bravo

AF:

0.000257

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.000382

EpiControl

AF:

0.000296

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:10

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

DNA ligase IV deficiency

Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 25, 2024	This sequence change creates a premature translational stop signal (p.Lys424Argfs*20) in the LIG4 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 488 amino acid(s) of the LIG4 protein. This variant is present in population databases (rs772226399, gnomAD 0.02%). This premature translational stop signal has been observed in individual(s) with clinical features of LIG4 syndrome (PMID: 16358631, 24123394, 27612988, 27893162, 29146883). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant is also known as K424fs. ClinVar contains an entry for this variant (Variation ID: 279838). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Institut de Recherche Interdisciplinaire en Biologie Humaine et Moleculaire, Universite Libre de Bruxelles	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein	Feb 17, 2021	ACMG classification criteria: PVS1 very strong, PS4 moderate, PM3 very strong, PP1 moderate -
Pathogenic, criteria provided, single submitter	clinical testing	Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago	May 18, 2018	LIG4 NM_002312.3 exon 2 p.Lys424Argfs*20 (c.1271_1275del): This variant has been reported as compound heterozygous in the literature in at least 11 individuals with features of LIG4 syndrome (most commonly immunodeficiency and failure to thrive), segregating with disease in at least 3 affected family members (Buck 2006 PMID:16358361, Enders 2006 PMID:16585603, Murray 2014 PMID:24123394, Cifaldi 2016 PMID:27893162, Jiang 2016 PMID:26762768, Walne 2016 PMID:27612988). This variant is present in 27/126568 European alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/rs772226399). Please note, disease causing variants may be present in control databases at low frequencies, reflective of the general population and/or variable expressivity. This variant is present in ClinVar, with several labs classifying this variant as pathogenic (Variation ID:279838). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. Of note, functional studies suggest that this variant may result in increased sensitivity to radiation (Buck 2006 PMID:16358361, Enders 2006 PMID:16585603, Murray 2014 PMID:24123394, Cifaldi 2016 PMID:27893162). This variant represents a deletion of 5 nucelotides and creates a premature stop codon 20 amino acids downstream from this location which results in an absent or abnormal protein. Loss of function variants have been reported in association with disease for this gene. In summary, this variant is classified as pathogenic. -

LIG4-related disorder

Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 28, 2017	The LIG4 c.1271_1275delAAAGA (p.Lys424ArgfsTer20) variant results in a frameshift and is predicted to result in premature termination of the protein. The p.Lys424ArgfsTer20 variant has been reported in five studies in which it is found in a compound heterozygous state in 14 individuals with LIG4-related disorders from 11 unrelated families (Buck et al. 2006; Enders et al. 2006; Murray et al. 2014; Jiang et al. 2016; Walne et al. 2016). In all cases, the p.Lys424ArgfsTer20 variant was inherited from a healthy heterozygous parent. Two of these patients were diagnosed with dyskeratosis congenita; the authors state that clinical symptoms in these patients had substantial overlap with LIG4 syndrome (Walne et al. 2016). Control data are unavailable for this variant, which is reported at a frequency of 0.00029 in the African population of the Exome Aggregation Consortium. Buck et al. (2006) showed that Lig4 protein expression in fibroblasts from one patient was significantly reduced compared to wild type, and a cell survival assay in fibroblasts from a second patient showed increased sensitivity to ionizing radiation. Based on the evidence and potential impact of frameshift variants, the p.Lys424ArgfsTer20 is classified as pathogenic for LIG4-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Pathogenic, criteria provided, single submitter	clinical testing	Genomic Research Center, Shahid Beheshti University of Medical Sciences	Dec 18, 2017	- -

not provided

Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2023	LIG4: PVS1, PM3, PM2:Supporting -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Oct 03, 2023	Published functional studies demonstrate a damaging effect on Lig4 protein levels (Buck et al., 2006); Frameshift variant predicted to result in protein truncation, as the last 488 amino acids are replaced with 19 different amino acids, and other loss-of-function variants have been reported downstream in the Human Gene Mutation Database (HGMD); This variant is associated with the following publications: (PMID: 27893162, 26762768, 16358361, 27612988, 16585603, 24123394, 30719430, 31696992, 31980526, 34426522, 29146883, 32471509, 31589614, 35595529, 34313030, 34630384, 35665479, 37437665, 36221079) -

Multiple myeloma;C1847827:DNA ligase IV deficiency

Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago	Mar 30, 2021	LIG4 NM_002312.3 exon 2 p.Lys424Argfs*20 (c.1271_1275del): This variant has been reported as compound heterozygous in the literature in at least 11 individuals with features of LIG4 syndrome (most commonly immunodeficiency and failure to thrive), segregating with disease in at least 3 affected family members (Buck 2006 PMID:16358361, Enders 2006 PMID:16585603, Murray 2014 PMID:24123394, Cifaldi 2016 PMID:27893162, Jiang 2016 PMID:26762768, Walne 2016 PMID:27612988). This variant is present in 27/126568 European alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/rs772226399). Please note, disease causing variants may be present in control databases at low frequencies, reflective of the general population and/or variable expressivity. This variant is present in ClinVar, with several labs classifying this variant as pathogenic (Variation ID:279838). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. Of note, functional studies suggest that this variant may result in increased sensitivity to radiation (Buck 2006 PMID:16358361, Enders 2006 PMID:16585603, Murray 2014 PMID:24123394, Cifaldi 2016 PMID:27893162). This variant represents a deletion of 5 nucelotides and creates a premature stop codon 20 amino acids downstream from this location which results in an absent or abnormal protein. Loss of function variants have been reported in association with disease for this gene. In summary, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Apr 18, 2022	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

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