chrX-115306349-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_016383.5(LUZP4):​c.487C>T​(p.Arg163*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000141 in 1,209,099 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000090 ( 0 hom., 0 hem., cov: 22)
Exomes 𝑓: 0.000015 ( 0 hom. 3 hem. )

Consequence

LUZP4
NM_016383.5 stop_gained

Scores

2
1
2

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.284
Variant links:
Genes affected
LUZP4 (HGNC:24971): (leucine zipper protein 4) This gene encodes a leucine-zipper protein that was first defined as a cancer testis antigens. The encoded protein is an RNA binding protein that interacts with the mRNA export receptor nuclear RNA export factor 2. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High Hemizygotes in GnomAdExome4 at 3 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LUZP4NM_016383.5 linkc.487C>T p.Arg163* stop_gained Exon 4 of 4 ENST00000371920.4 NP_057467.1 Q9P127-1
LUZP4NM_001318840.2 linkc.241C>T p.Arg81* stop_gained Exon 3 of 3 NP_001305769.1 Q9P127-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LUZP4ENST00000371920.4 linkc.487C>T p.Arg163* stop_gained Exon 4 of 4 1 NM_016383.5 ENSP00000360988.3 Q9P127-1
LUZP4ENST00000371921.5 linkc.*131C>T 3_prime_UTR_variant Exon 3 of 3 2 ENSP00000360989.1 Q5JX98

Frequencies

GnomAD3 genomes
AF:
0.00000901
AC:
1
AN:
110953
Hom.:
0
Cov.:
22
AF XY:
0.00
AC XY:
0
AN XY:
33179
show subpopulations
Gnomad AFR
AF:
0.0000328
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000545
AC:
1
AN:
183363
Hom.:
0
AF XY:
0.0000147
AC XY:
1
AN XY:
67815
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:
0.0000524
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000146
AC:
16
AN:
1098146
Hom.:
0
Cov.:
31
AF XY:
0.00000825
AC XY:
3
AN XY:
363500
show subpopulations
Gnomad4 AFR exome
AF:
0.0000757
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000185
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000143
Gnomad4 OTH exome
AF:
0.0000217
GnomAD4 genome
AF:
0.00000901
AC:
1
AN:
110953
Hom.:
0
Cov.:
22
AF XY:
0.00
AC XY:
0
AN XY:
33179
show subpopulations
Gnomad4 AFR
AF:
0.0000328
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000151
ExAC
AF:
0.0000165
AC:
2
EpiCase
AF:
0.0000545
EpiControl
AF:
0.0000593

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Uncertain:1
Oct 01, 2019
CeGaT Center for Human Genetics Tuebingen
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.19
D
BayesDel_noAF
Pathogenic
0.18
CADD
Uncertain
23
DANN
Uncertain
0.99
FATHMM_MKL
Benign
0.035
N
Vest4
0.060
GERP RS
-2.8

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: rs781872800; hg19: chrX-114540914; COSMIC: COSV64218557; API