rs17010022
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_032603.5(LOXL3):āc.1113G>Cā(p.Leu371=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0156 in 1,613,850 control chromosomes in the GnomAD database, including 2,773 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.023 ( 393 hom., cov: 32)
Exomes š: 0.015 ( 2380 hom. )
Consequence
LOXL3
NM_032603.5 synonymous
NM_032603.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.28
Genes affected
LOXL3 (HGNC:13869): (lysyl oxidase like 3) This gene encodes a lysyl oxidase, which likely functions as an amine oxidase and plays a role in the formation of crosslinks in collagens and elastin. Deletion of the related gene in mouse causes neonatal mortality with cleft palate, spine deformity, and defects in collagen organization. A mutation in this gene was found in a family with Stickler syndrome. [provided by RefSeq, Sep 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
?
Variant 2-74536131-C-G is Benign according to our data. Variant chr2-74536131-C-G is described in ClinVar as [Benign]. Clinvar id is 1239926.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=3.28 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOXL3 | NM_032603.5 | c.1113G>C | p.Leu371= | synonymous_variant | 7/14 | ENST00000264094.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LOXL3 | ENST00000264094.8 | c.1113G>C | p.Leu371= | synonymous_variant | 7/14 | 1 | NM_032603.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0227 AC: 3457AN: 152168Hom.: 389 Cov.: 32
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GnomAD3 exomes AF: 0.0495 AC: 12431AN: 251136Hom.: 1541 AF XY: 0.0429 AC XY: 5830AN XY: 135762
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GnomAD4 exome AF: 0.0148 AC: 21689AN: 1461564Hom.: 2380 Cov.: 33 AF XY: 0.0142 AC XY: 10322AN XY: 727116
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GnomAD4 genome ? AF: 0.0227 AC: 3464AN: 152286Hom.: 393 Cov.: 32 AF XY: 0.0254 AC XY: 1894AN XY: 74444
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 21, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at