Variant X-115306328-AATC-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PM4_SupportingBP6_ModerateBS2

The NM_016383.5(LUZP4):c.472_474del(p.His158del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000658 in 1,209,434 control chromosomes in the GnomAD database, including 1 homozygotes. There are 245 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00050 ( 0 hom., 22 hem., cov: 22)

Exomes 𝑓: 0.00067 ( 1 hom. 223 hem. )

Consequence

LUZP4
NM_016383.5 inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0330

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]

LUZP4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_016383.5. Strenght limited to Supporting due to length of the change: 1aa.

BP6

Variant X-115306328-AATC-A is Benign according to our data. Variant chrX-115306328-AATC-A is described in ClinVar as [Likely_benign]. Clinvar id is 2661249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-115306328-AATC-A is described in Lovd as [Likely_benign].

BS2

High Hemizygotes in GnomAd4 at 22 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LUZP4	NM_016383.5 linkuse as main transcript	c.472_474del	p.His158del	inframe_deletion	4/4	ENST00000371920.4	NP_057467.1
LUZP4	NM_001318840.2 linkuse as main transcript	c.226_228del	p.His76del	inframe_deletion	3/3		NP_001305769.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LUZP4	ENST00000371920.4 linkuse as main transcript	c.472_474del	p.His158del	inframe_deletion	4/4	1	NM_016383.5	ENSP00000360988	P1	Q9P127-1
LUZP4	ENST00000371921.5 linkuse as main transcript	c.116_118del		3_prime_UTR_variant	3/3	2		ENSP00000360989

Frequencies

GnomAD3 genomes

AF:

0.000504

AC:

AN:

111193

Hom.:

Cov.:

AF XY:

0.000659

AC XY:

AN XY:

33365

show subpopulations

Gnomad AFR

AF:

0.000163

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.000377

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000942

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000311

AC:

AN:

183381

Hom.:

AF XY:

0.000265

AC XY:

AN XY:

67829

show subpopulations

Gnomad AFR exome

AF:

0.000152

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.000267

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0000625

Gnomad NFE exome

AF:

0.000623

Gnomad OTH exome

AF:

0.000221

GnomAD4 exome

AF:

0.000674

AC:

740

AN:

1098187

Hom.:

AF XY:

0.000613

AC XY:

223

AN XY:

363543

show subpopulations

Gnomad4 AFR exome

AF:

0.0000758

Gnomad4 AMR exome

AF:

0.0000568

Gnomad4 ASJ exome

AF:

0.000464

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0000494

Gnomad4 NFE exome

AF:

0.000848

Gnomad4 OTH exome

AF:

0.000239

GnomAD4 genome

AF:

0.000503

AC:

AN:

111247

Hom.:

Cov.:

AF XY:

0.000658

AC XY:

AN XY:

33429

show subpopulations

Gnomad4 AFR

AF:

0.000163

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.000377

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000942

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000473

Hom.:

Bravo

AF:

0.000419

EpiCase

AF:

0.000436

EpiControl

AF:

0.000237

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2023

LUZP4: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over