8-97775926-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000445593.6(LAPTM4B):​c.190C>T​(p.Gln64*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000191 in 1,045,298 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000019 ( 0 hom. )

Consequence

LAPTM4B
ENST00000445593.6 stop_gained

Scores

2
1
4

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00
Variant links:
Genes affected
LAPTM4B (HGNC:13646): (lysosomal protein transmembrane 4 beta) Enables ceramide binding activity; enzyme binding activity; and phosphatidylinositol bisphosphate binding activity. Involved in several processes, including negative regulation of macromolecule metabolic process; regulation of lysosomal membrane permeability; and regulation of lysosome organization. Located in several cellular components, including endosome; lysosomal membrane; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LAPTM4BNM_018407.6 linkc.-84C>T 5_prime_UTR_variant Exon 1 of 7 ENST00000521545.7 NP_060877.4 Q86VI4-2
LOC124901986XR_007061020.1 linkn.-151G>A upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LAPTM4BENST00000445593.6 linkc.190C>T p.Gln64* stop_gained Exon 1 of 7 1 ENSP00000402301.2 Q86VI4-3
LAPTM4BENST00000619747.1 linkc.190C>T p.Gln64* stop_gained Exon 1 of 7 1 ENSP00000482533.1 Q86VI4-3
LAPTM4BENST00000521545 linkc.-84C>T 5_prime_UTR_variant Exon 1 of 7 1 NM_018407.6 ENSP00000428409.1 Q86VI4-2
LAPTM4BENST00000517924 linkc.-84C>T 5_prime_UTR_variant Exon 1 of 5 5 ENSP00000429868.2 H0YBN1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.0000184
AC:
1
AN:
54450
Hom.:
0
AF XY:
0.0000314
AC XY:
1
AN XY:
31804
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000110
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000191
AC:
2
AN:
1045298
Hom.:
0
Cov.:
33
AF XY:
0.00000387
AC XY:
2
AN XY:
516306
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:
0.0000179
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000122
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.36
D
BayesDel_noAF
Pathogenic
0.27
CADD
Benign
12
DANN
Uncertain
0.99
Eigen
Benign
0.071
Eigen_PC
Benign
-0.28
FATHMM_MKL
Benign
0.11
N
Vest4
0.32
GERP RS
3.2
RBP_binding_hub_radar
0.92
RBP_regulation_power_radar
2.0

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs760702744; hg19: chr8-98788154; API