NM_206937.2(LIG4):c.1932A>C (p.Leu644Phe) AND DNA ligase IV deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 27, 2022
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:: RCV001926487.6

Allele description [Variation Report for NM_206937.2(LIG4):c.1932A>C (p.Leu644Phe)]

NM_206937.2(LIG4):c.1932A>C (p.Leu644Phe)

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.1932A>C (p.Leu644Phe)

HGVS:

NC_000013.11:g.108209337T>G
NG_007396.1:g.11198A>C
NM_001098268.2:c.1932A>C
NM_001330595.2:c.1731A>C
NM_001352598.2:c.1932A>C
NM_001352599.2:c.1932A>C
NM_001352600.2:c.1932A>C
NM_001352601.2:c.1932A>C
NM_001352602.2:c.1932A>C
NM_001352603.1:c.1932A>C
NM_001352604.2:c.1968A>C
NM_001379095.1:c.1932A>C
NM_002312.3:c.1932A>C
NM_206937.2:c.1932A>CMANE SELECT
NP_001091738.1:p.Leu644Phe
NP_001317524.1:p.Leu577Phe
NP_001339527.1:p.Leu644Phe
NP_001339528.1:p.Leu644Phe
NP_001339529.1:p.Leu644Phe
NP_001339530.1:p.Leu644Phe
NP_001339531.1:p.Leu644Phe
NP_001339532.1:p.Leu644Phe
NP_001339533.1:p.Leu656Phe
NP_001366024.1:p.Leu644Phe
NP_002303.2:p.Leu644Phe
NP_996820.1:p.Leu644Phe
LRG_79t1:c.1932A>C
LRG_79:g.11198A>C
LRG_79p1:p.Leu644Phe
NC_000013.10:g.108861685T>G

Protein change:

L577F

Links:

dbSNP: rs2138970296

NCBI 1000 Genomes Browser:

rs2138970296

Molecular consequence:

NM_001098268.2:c.1932A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001330595.2:c.1731A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001352598.2:c.1932A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001352599.2:c.1932A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001352600.2:c.1932A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001352601.2:c.1932A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001352602.2:c.1932A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001352603.1:c.1932A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001352604.2:c.1968A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001379095.1:c.1932A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_002312.3:c.1932A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_206937.2:c.1932A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: DNA ligase IV deficiency
Synonyms:: Lig4 syndrome
Identifiers:: MONDO: MONDO:0011686; MedGen: C1847827; Orphanet: 99812; OMIM: 606593

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002199971	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 27, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002199971

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 27, 2022)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002199971.3

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

Description

This variant has not been reported in the literature in individuals affected with LIG4-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The phenylalanine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces leucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 644 of the LIG4 protein (p.Leu644Phe).

#	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

Last Updated: Sep 29, 2024

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