chr10-98256815-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_032211.7(LOXL4):c.1393C>G(p.Gln465Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000478 in 1,614,174 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q465H) has been classified as Uncertain significance.
Frequency
Consequence
NM_032211.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOXL4 | NM_032211.7 | c.1393C>G | p.Gln465Glu | missense_variant | 9/15 | ENST00000260702.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LOXL4 | ENST00000260702.4 | c.1393C>G | p.Gln465Glu | missense_variant | 9/15 | 1 | NM_032211.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000207 AC: 52AN: 251132Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135792
GnomAD4 exome AF: 0.000504 AC: 737AN: 1461808Hom.: 0 Cov.: 31 AF XY: 0.000461 AC XY: 335AN XY: 727216
GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152366Hom.: 0 Cov.: 33 AF XY: 0.000242 AC XY: 18AN XY: 74518
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.1393C>G (p.Q465E) alteration is located in exon 9 (coding exon 8) of the LOXL4 gene. This alteration results from a C to G substitution at nucleotide position 1393, causing the glutamine (Q) at amino acid position 465 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at