1-26282386-GCCGGGA-G

Position:

• chr1-26282386-GCCGGGA-G

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP3 BA1

The NM_001389556.1(UBXN11):​c.1470_1475del​(p.Gly492_Pro493del) variant causes a 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 inframe_deletion
• Clinical Significance: Pathogenic no assertion criteria provided P:3
• Conservation: PhyloP100: 1.61

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]

ACMG classification

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	UniProt
UBXN11	NM_001389556.1	c.1470_1475del	p.Gly492_Pro493del	inframe_deletion	15/15	ENST00000374222.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBXN11	ENST00000374222.6	c.1470_1475del	p.Gly492_Pro493del	inframe_deletion	15/15	5	NM_001389556.1	A2

Frequencies

GnomAD3 genomes AF: 0.241 AC: 23242 AN: 96358 Hom.: 2057 Cov.: 0

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

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

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.: 0 AF XY: 0.242 AC XY: 11295 AN XY: 46656

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

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

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs140364749; hg19: chr1-26608877;