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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:
37

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000170138GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Benign
(Jan 31, 2013)
germlineclinical testing

Citation Link,

SCV000308821PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)
Benigngermlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000539534Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)
Benign
(Mar 29, 2016)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001742504Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus
no assertion criteria provided
Benigngermlineclinical testing

SCV002051451Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Likely benign
(Dec 3, 2021)
germlineclinical testing

Citation Link,

SCV004102287Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan
criteria provided, single submitter

(ACMG Guidelines, 2015)
Benign
(Nov 12, 2023)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineno37not providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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

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

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

From PreventionGenetics, part of Exact Sciences, SCV000308821.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

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

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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)

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

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

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

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

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

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

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided37not providednot providedclinical 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot provided37not providednot providednot provided

Last Updated: Sep 29, 2024