18-79973765-C-A
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1_StrongPM2PP5_Very_Strong
The NM_006701.5(TXNL4A):c.349G>T(p.Glu117*) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000274 in 1,461,894 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_006701.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461894Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727248
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Choanal atresia-hearing loss-cardiac defects-craniofacial dysmorphism syndrome Pathogenic:2Other:1
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TXNL4A-related disorder Pathogenic:1
The TXNL4A c.349G>T variant is predicted to result in premature protein termination (p.Glu117*). This variant was reported in the compound heterozygous state in two siblings with Burn-McKeown syndrome (Wieczorek et al 2014. PubMed ID: 25434003; Wieczorek D et al 2003. PubMed ID: 14564154). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Nonsense variants in TXNL4A are expected to be pathogenic. This variant is interpreted as pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at