NM_206937.2(LIG4):c.26C>T (p.Thr9Ile) AND not specified

Germline classification:: Benign/Likely benign (6 submissions)
Last evaluated:: Nov 12, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000126631.15

Allele description [Variation Report for NM_206937.2(LIG4):c.26C>T (p.Thr9Ile)]

NM_206937.2(LIG4):c.26C>T (p.Thr9Ile)

Gene:

LIG4:DNA ligase 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

13q33.3

Genomic location:

Preferred name:

NM_206937.2(LIG4):c.26C>T (p.Thr9Ile)

Other names:

p.T9I:ACT>ATT

HGVS:

NC_000013.11:g.108211243G>A
NG_007396.1:g.9292C>T
NM_001098268.2:c.26C>T
NM_001330595.2:c.-149-27C>T
NM_001352598.2:c.26C>T
NM_001352599.2:c.26C>T
NM_001352600.2:c.26C>T
NM_001352601.2:c.26C>T
NM_001352602.2:c.26C>T
NM_001352603.1:c.26C>T
NM_001352604.2:c.89-27C>T
NM_001379095.1:c.26C>T
NM_002312.3:c.26C>T
NM_206937.2:c.26C>TMANE SELECT
NP_001091738.1:p.Thr9Ile
NP_001339527.1:p.Thr9Ile
NP_001339528.1:p.Thr9Ile
NP_001339529.1:p.Thr9Ile
NP_001339530.1:p.Thr9Ile
NP_001339531.1:p.Thr9Ile
NP_001339532.1:p.Thr9Ile
NP_001366024.1:p.Thr9Ile
NP_002303.2:p.Thr9Ile
NP_996820.1:p.Thr9Ile
LRG_79t1:c.26C>T
LRG_79:g.9292C>T
LRG_79p1:p.Thr9Ile
NC_000013.10:g.108863591G>A
NM_206937.1:c.26C>T
P49917:p.Thr9Ile

Protein change:

T9I; THR9ILE

Links:

UniProtKB: P49917#VAR_033884; OMIM: 601837.0006; dbSNP: rs1805388

NCBI 1000 Genomes Browser:

rs1805388

Molecular consequence:

NM_001330595.2:c.-149-27C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001352604.2:c.89-27C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001098268.2:c.26C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352598.2:c.26C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352599.2:c.26C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352600.2:c.26C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352601.2:c.26C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352602.2:c.26C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352603.1:c.26C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379095.1:c.26C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_002312.3:c.26C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_206937.2:c.26C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000170138	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Jan 31, 2013)	germline	clinical testing	Citation Link,
SCV000308821	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000539534	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Mar 29, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001742504	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Benign	germline	clinical testing
SCV002051451	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely benign (Dec 3, 2021)	germline	clinical testing	Citation Link,
SCV004102287	Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Nov 12, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	37	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From GeneDx, SCV000170138.10

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	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

From PreventionGenetics, part of Exact Sciences, SCV000308821.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

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

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000539534.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency, Clinvar assertions are benign and protective (not pathogenic)

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

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001742504.3

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

#	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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002051451.1

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

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

From Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan, SCV004102287.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	37	not provided	not provided	clinical testing	PubMed (1)

Description

This variant is classified as Benign based on local population frequency. This variant was detected in 39% of patients studied by a panel of primary immunodeficiencies. Number of patients: 37. Only high quality variants are reported.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		37	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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