Variant rs714909 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000266269.10(PATZ1):c.522C>T(p.Leu174=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 1,614,008 control chromosomes in the GnomAD database, including 60,480 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.21 ( 4336 hom., cov: 33)

Exomes 𝑓: 0.27 ( 56144 hom. )

Consequence

PATZ1
ENST00000266269.10 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.480

Variant links:

Genes affected

PATZ1 (HGNC:13071): (POZ/BTB and AT hook containing zinc finger 1) The protein encoded by this gene contains an A-T hook DNA binding motif which usually binds to other DNA binding structures to play an important role in chromatin modeling and transcription regulation. Its Poz domain is thought to function as a site for protein-protein interaction and is required for transcriptional repression, and the zinc-fingers comprise the DNA binding domain. Since the encoded protein has typical features of a transcription factor, it is postulated to be a repressor of gene expression. In small round cell sarcoma, this gene is fused to EWS by a small inversion of 22q, then the hybrid is thought to be translocated (t(1;22)(p36.1;q12). The rearrangement of chromosome 22 involves intron 8 of EWS and exon 1 of this gene creating a chimeric sequence containing the transactivation domain of EWS fused to zinc finger domain of this protein. This is a distinct example of an intra-chromosomal rearrangement of chromosome 22. Four alternatively spliced transcript variants are described for this gene. [provided by RefSeq, Jul 2008]

PATZ1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP7

Synonymous conserved (PhyloP=-0.48 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
PATZ1	NM_014323.3 linkuse as main transcript	c.522C>T	p.Leu174=	synonymous_variant	1/5	ENST00000266269.10	NP_055138.2
PATZ1	NM_032050.2 linkuse as main transcript	c.522C>T	p.Leu174=	synonymous_variant	1/4		NP_114439.1
PATZ1	NM_032051.2 linkuse as main transcript	c.522C>T	p.Leu174=	synonymous_variant	1/3		NP_114440.1
PATZ1	NM_032052.2 linkuse as main transcript	c.522C>T	p.Leu174=	synonymous_variant	1/5		NP_114441.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PATZ1	ENST00000266269.10 linkuse as main transcript	c.522C>T	p.Leu174=	synonymous_variant	1/5	1	NM_014323.3	ENSP00000266269	P1	Q9HBE1-1
PATZ1	ENST00000351933.8 linkuse as main transcript	c.522C>T	p.Leu174=	synonymous_variant	1/4	1		ENSP00000337520		Q9HBE1-3
PATZ1	ENST00000215919.3 linkuse as main transcript	c.522C>T	p.Leu174=	synonymous_variant	1/3	1		ENSP00000215919		Q9HBE1-4
PATZ1	ENST00000405309.7 linkuse as main transcript	c.522C>T	p.Leu174=	synonymous_variant	1/5	1		ENSP00000384173		Q9HBE1-2

Frequencies

GnomAD3 genomes

AF:

0.210

AC:

31983

AN:

152102

Hom.:

4332

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0528

Gnomad AMI

AF:

0.285

Gnomad AMR

AF:

0.236

Gnomad ASJ

AF:

0.193

Gnomad EAS

AF:

0.122

Gnomad SAS

AF:

0.211

Gnomad FIN

AF:

0.343

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.287

Gnomad OTH

AF:

0.194

GnomAD3 exomes

AF:

0.246

AC:

61691

AN:

251174

Hom.:

8433

AF XY:

0.247

AC XY:

33582

AN XY:

135834

show subpopulations

Gnomad AFR exome

AF:

0.0460

Gnomad AMR exome

AF:

0.270

Gnomad ASJ exome

AF:

0.180

Gnomad EAS exome

AF:

0.138

Gnomad SAS exome

AF:

0.214

Gnomad FIN exome

AF:

0.341

Gnomad NFE exome

AF:

0.280

Gnomad OTH exome

AF:

0.239

GnomAD4 exome

AF:

0.271

AC:

395710

AN:

1461788

Hom.:

56144

Cov.:

AF XY:

0.268

AC XY:

195225

AN XY:

727208

show subpopulations

Gnomad4 AFR exome

AF:

0.0423

Gnomad4 AMR exome

AF:

0.269

Gnomad4 ASJ exome

AF:

0.183

Gnomad4 EAS exome

AF:

0.116

Gnomad4 SAS exome

AF:

0.218

Gnomad4 FIN exome

AF:

0.343

Gnomad4 NFE exome

AF:

0.288

Gnomad4 OTH exome

AF:

0.244

GnomAD4 genome

AF:

0.210

AC:

31993

AN:

152220

Hom.:

4336

Cov.:

AF XY:

0.213

AC XY:

15816

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.0526

Gnomad4 AMR

AF:

0.237

Gnomad4 ASJ

AF:

0.193

Gnomad4 EAS

AF:

0.122

Gnomad4 SAS

AF:

0.213

Gnomad4 FIN

AF:

0.343

Gnomad4 NFE

AF:

0.287

Gnomad4 OTH

AF:

0.192

Alfa

AF:

0.249

Hom.:

2877

Bravo

AF:

0.195

Asia WGS

AF:

0.142

AC:

494

AN:

3478

EpiCase

AF:

0.260

EpiControl

AF:

0.254

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

6.6

DANN

Benign

0.94

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over