18-46610789-C-T
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_001384474.1(LOXHD1):c.746G>A(p.Trp249Ter) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000715 in 1,398,912 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 Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001384474.1 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOXHD1 | NM_001384474.1 | c.746G>A | p.Trp249Ter | stop_gained | 6/41 | ENST00000642948.1 | NP_001371403.1 | |
LOXHD1 | NM_144612.7 | c.746G>A | p.Trp249Ter | stop_gained | 6/40 | NP_653213.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LOXHD1 | ENST00000642948.1 | c.746G>A | p.Trp249Ter | stop_gained | 6/41 | NM_001384474.1 | ENSP00000496347 | P1 | ||
LOXHD1 | ENST00000536736.5 | c.746G>A | p.Trp249Ter | stop_gained | 6/40 | 5 | ENSP00000444586 | |||
LOXHD1 | ENST00000441551.6 | c.746G>A | p.Trp249Ter | stop_gained | 6/39 | 5 | ENSP00000387621 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 7.15e-7 AC: 1AN: 1398912Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 689916
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Deafness Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues | Jul 30, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at