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GeneBe

rs1048661

chr15-73927205-G-Achr15-73927205-G-T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PM2_SupportingBP4_Moderate

The NM_005576(LOXL1):c.422G>A(p.Arg141Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign 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. R141L) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

LOXL1
NM_005576 missense

Scores

2
1
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.83

Links

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 33.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.15081781).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOXL1NM_005576.4 linkuse as main transcriptc.422G>A p.Arg141Gln missense_variant 1/7 ENST00000261921.8
LOXL1-AS1NR_040069.1 linkuse as main transcriptn.184+860C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LOXL1ENST00000261921.8 linkuse as main transcriptc.422G>A p.Arg141Gln missense_variant 1/71 NM_005576.4 P1
LOXL1-AS1ENST00000685373.1 linkuse as main transcriptn.198+572C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.95e-7
AC:
1
AN:
1439534
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
716566
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.04e-7
Gnomad4 OTH exome
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.23
BayesDel_addAF
Benign
-0.26
T
BayesDel_noAF
Benign
-0.62
Cadd
Benign
23
Dann
Pathogenic
1.0
DEOGEN2
Benign
0.093
T
Eigen
Benign
-0.052
Eigen_PC
Benign
0.061
FATHMM_MKL
Benign
0.66
D
LIST_S2
Benign
0.79
T
M_CAP
Uncertain
0.15
D
MetaRNN
Benign
0.15
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.97
L
MutationTaster
Benign
0.75
N
PrimateAI
Pathogenic
0.88
D
PROVEAN
Benign
-0.59
N
REVEL
Benign
0.056
Sift
Benign
0.073
T
Sift4G
Benign
0.50
T
Polyphen
0.28
B
Vest4
0.028
MutPred
0.21
Loss of methylation at R141 (P = 0.0102);
MVP
0.39
ClinPred
0.61
D
GERP RS
4.1
Varity_R
0.22
gMVP
0.29

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1048661; hg19: chr15-74219546;