rs187658135
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001384474.1(LOXHD1):c.1571G>T(p.Arg524Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000193 in 1,552,084 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R524C) has been classified as Likely benign.
Frequency
Consequence
NM_001384474.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOXHD1 | NM_001384474.1 | c.1571G>T | p.Arg524Leu | missense_variant | 12/41 | ENST00000642948.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LOXHD1 | ENST00000642948.1 | c.1571G>T | p.Arg524Leu | missense_variant | 12/41 | NM_001384474.1 | P1 | ||
LOXHD1 | ENST00000536736.5 | c.1571G>T | p.Arg524Leu | missense_variant | 12/40 | 5 | |||
LOXHD1 | ENST00000441551.6 | c.1571G>T | p.Arg524Leu | missense_variant | 12/39 | 5 | |||
LOXHD1 | ENST00000335730.6 | n.884G>T | non_coding_transcript_exon_variant | 5/27 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000143 AC: 2AN: 1399904Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 690434
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at