rs727504468
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001384474.1(LOXHD1):c.3145G>A(p.Glu1049Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000572 in 1,399,756 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E1049G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001384474.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOXHD1 | NM_001384474.1 | c.3145G>A | p.Glu1049Lys | missense_variant | 20/41 | ENST00000642948.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LOXHD1 | ENST00000642948.1 | c.3145G>A | p.Glu1049Lys | missense_variant | 20/41 | NM_001384474.1 | P1 | ||
LOXHD1 | ENST00000536736.5 | c.3145G>A | p.Glu1049Lys | missense_variant | 20/40 | 5 | |||
LOXHD1 | ENST00000441551.6 | c.2599-2030G>A | intron_variant | 5 | |||||
LOXHD1 | ENST00000335730.6 | n.2458G>A | non_coding_transcript_exon_variant | 13/27 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000572 AC: 8AN: 1399756Hom.: 0 Cov.: 33 AF XY: 0.0000101 AC XY: 7AN XY: 690376
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Sep 09, 2014 | Variant classified as Uncertain Significance - Favor Benign. The Glu1049Lys vari ant in LOXHD1 has been previously reported in 1 individual with hearing loss who was homozygous for a pathogenic variant in another gene that explained their he aring loss (LMM unpublished data). This variant was absent from large population studies. Computational prediction tools and conservation analyses do not provid e strong support for or against an impact to the protein. In summary, the clinic al significance of the Glu1049Lys variant is uncertain. - |
Autosomal recessive nonsyndromic hearing loss 77 Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 1049 of the LOXHD1 protein (p.Glu1049Lys). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with LOXHD1-related conditions. ClinVar contains an entry for this variant (Variation ID: 178821). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at