Total submissions: 3
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Labcorp Genetics |
RCV001240625 | SCV001413591 | likely benign | DNA ligase IV deficiency | 2025-01-23 | criteria provided, single submitter | clinical testing | |
| Mayo Clinic Laboratories, |
RCV001507830 | SCV001713646 | uncertain significance | not provided | 2020-10-29 | criteria provided, single submitter | clinical testing | |
| Women's Health and Genetics/Laboratory Corporation of America, |
RCV003317465 | SCV004020871 | likely benign | not specified | 2023-06-30 | criteria provided, single submitter | clinical testing | Variant summary: LIG4 c.1236T>A (p.Asn412Lys) results in a non-conservative amino acid change located in the central domain (IPR012310) of the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0001 in 249860 control chromosomes, predominantly at a frequency of 0.00072 within the Latino subpopulation in the gnomAD database. The observed variant frequency within Latino control individuals in the gnomAD database is approximately 2.036 fold of the estimated maximal expected allele frequency for a pathogenic variant in LIG4 causing Severe Combined Immunodeficiency phenotype (0.00035), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Latino origin. c.1236T>A has been reported in the literature in at least one individual affected with features of LIG4 deficiency (e.g., Boone_2019), however without strong evidence for causality (e.g., inconsistencies in described genotype and lack of co-segregation data). This report therefore does not provide unequivocal conclusions about association of the variant with Severe Combined Immunodeficiency. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication was ascertained in the context of this evaluation (PMID: 30719430). Two submitters have reported clinical-significance assessments for this variant to ClinVar after 2014. One submitter classified the variant as likely benign, and one submitter classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as likely benign. |