rs1182325987
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_001384474.1(LOXHD1):āc.4147A>Gā(p.Thr1383Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000238 in 1,551,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T1383R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001384474.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOXHD1 | NM_001384474.1 | c.4147A>G | p.Thr1383Ala | missense_variant | 27/41 | ENST00000642948.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LOXHD1 | ENST00000642948.1 | c.4147A>G | p.Thr1383Ala | missense_variant | 27/41 | NM_001384474.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 19AN: 159038Hom.: 0 AF XY: 0.000108 AC XY: 9AN XY: 83700
GnomAD4 exome AF: 0.0000207 AC: 29AN: 1399466Hom.: 0 Cov.: 30 AF XY: 0.0000188 AC XY: 13AN XY: 690232
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74414
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 20, 2016 | p.Thr1383Ala in exon 27 of LOXHD1: This variant is not expected to have clinical significance due to a lack of conservation across species, including mammals. O f note, three mammals (opossum, Tasmanian devil, wallaby) have an alanine (Ala) at this position despite high nearby amino acid conservation. In addition, compu tational prediction tools do not suggest a high likelihood of impact to the prot ein. - |
LOXHD1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 02, 2024 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at