Variant 1-26282386-GCCGGGA-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP3BA1

The NM_001389556.1(UBXN11):c.1470_1475delTCCCGG(p.Pro491_Gly492del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.24 ( 2059 hom., cov: 0)

Exomes 𝑓: 0.28 ( 18623 hom. )

Failed GnomAD Quality Control

Consequence

UBXN11
NM_001389556.1 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:3

Conservation

PhyloP100: 1.61

Variant links:

Genes affected

UBXN11 (HGNC:30600): (UBX domain protein 11) This gene encodes a protein with a divergent C-terminal UBX domain. The homologous protein in the rat interacts with members of the Rnd subfamily of Rho GTPases at the cell periphery through its C-terminal region. It also interacts with several heterotrimeric G proteins through their G-alpha subunits and promotes Rho GTPase activation. It is proposed to serve a bidirectional role in the promotion and inhibition of Rho activity through upstream signaling pathways. The 3' coding sequence of this gene contains a polymoprhic region of 24 nt tandem repeats. Several transcripts containing between 1.5 and five repeat units have been reported. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

UBXN11 links:

UBXN11 (HGNC:):

UBXN11 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001389556.1

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBXN11	NM_001389556.1 linkuse as main transcript	c.1470_1475delTCCCGG	p.Pro491_Gly492del	disruptive_inframe_deletion	15/15	ENST00000374222.6	NP_001376485.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBXN11	ENST00000374222.6 linkuse as main transcript	c.1470_1475delTCCCGG	p.Pro491_Gly492del	disruptive_inframe_deletion	15/15	5	NM_001389556.1	ENSP00000363339.1		Q5T124-1

Frequencies

GnomAD3 genomes

AF:

0.241

AC:

23242

AN:

96358

Hom.:

2057

Cov.:

show subpopulations

Gnomad AFR

AF:

0.290

Gnomad AMI

AF:

0.236

Gnomad AMR

AF:

0.180

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.0269

Gnomad SAS

AF:

0.185

Gnomad FIN

AF:

0.296

Gnomad MID

AF:

0.279

Gnomad NFE

AF:

0.242

Gnomad OTH

AF:

0.217

GnomAD3 exomes

AF:

0.0867

AC:

10960

AN:

126364

Hom.:

1452

AF XY:

0.0845

AC XY:

5816

AN XY:

68848

show subpopulations

Gnomad AFR exome

AF:

0.139

Gnomad AMR exome

AF:

0.0389

Gnomad ASJ exome

AF:

0.0688

Gnomad EAS exome

AF:

0.00781

Gnomad SAS exome

AF:

0.0613

Gnomad FIN exome

AF:

0.151

Gnomad NFE exome

AF:

0.102

Gnomad OTH exome

AF:

0.100

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.284

AC:

200749

AN:

707630

Hom.:

18623

AF XY:

0.283

AC XY:

96889

AN XY:

342346

show subpopulations

Gnomad4 AFR exome

AF:

0.288

Gnomad4 AMR exome

AF:

0.0954

Gnomad4 ASJ exome

AF:

0.322

Gnomad4 EAS exome

AF:

0.0175

Gnomad4 SAS exome

AF:

0.209

Gnomad4 FIN exome

AF:

0.448

Gnomad4 NFE exome

AF:

0.295

Gnomad4 OTH exome

AF:

0.296

GnomAD4 genome

AF:

0.241

AC:

23249

AN:

96420

Hom.:

2059

Cov.:

AF XY:

0.242

AC XY:

11295

AN XY:

46656

show subpopulations

Gnomad4 AFR

AF:

0.290

Gnomad4 AMR

AF:

0.179

Gnomad4 ASJ

AF:

0.236

Gnomad4 EAS

AF:

0.0270

Gnomad4 SAS

AF:

0.186

Gnomad4 FIN

AF:

0.296

Gnomad4 NFE

AF:

0.242

Gnomad4 OTH

AF:

0.214

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:3

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Small cell lung carcinoma

Pathogenic:1

Pathogenic, no assertion criteria provided

research

Arun Kumar Laboratory, Indian Institute of Science

Jun 15, 2021

- -

Lung cancer

Pathogenic:1

Pathogenic, no assertion criteria provided

research

Arun Kumar Laboratory, Indian Institute of Science

Jun 15, 2021

- -

Hepatocellular carcinoma

Pathogenic:1

Pathogenic, no assertion criteria provided

research

Arun Kumar Laboratory, Indian Institute of Science

Jun 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

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