9-83707620-G-C
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_013438.5(UBQLN1):āc.60C>Gā(p.Ala20Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000126 in 1,583,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.000033 ( 0 hom., cov: 32)
Exomes š: 0.000010 ( 0 hom. )
Consequence
UBQLN1
NM_013438.5 synonymous
NM_013438.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.457
Genes affected
UBQLN1 (HGNC:12508): (ubiquilin 1) This gene encodes an ubiquitin-like protein (ubiquilin) that shares a high degree of similarity with related products in yeast, rat and frog. Ubiquilins contain an N-terminal ubiquitin-like domain and a C-terminal ubiquitin-associated domain. They physically associate with both proteasomes and ubiquitin ligases, and thus are thought to functionally link the ubiquitination machinery to the proteasome to affect in vivo protein degradation. This ubiquilin has also been shown to modulate accumulation of presenilin proteins, and it is found in lesions associated with Alzheimer's and Parkinson's disease. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant 9-83707620-G-C is Benign according to our data. Variant chr9-83707620-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 739713.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.457 with no splicing effect.
BS2
High AC in GnomAd4 at 5 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UBQLN1 | NM_013438.5 | c.60C>G | p.Ala20Ala | synonymous_variant | 1/11 | ENST00000376395.9 | NP_038466.2 | |
UBQLN1 | NM_053067.3 | c.60C>G | p.Ala20Ala | synonymous_variant | 1/10 | NP_444295.1 | ||
UBQLN1 | XM_005251948.4 | c.60C>G | p.Ala20Ala | synonymous_variant | 1/8 | XP_005252005.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UBQLN1 | ENST00000376395.9 | c.60C>G | p.Ala20Ala | synonymous_variant | 1/11 | 1 | NM_013438.5 | ENSP00000365576.4 | ||
UBQLN1 | ENST00000257468.11 | c.60C>G | p.Ala20Ala | synonymous_variant | 1/10 | 1 | ENSP00000257468.7 | |||
UBQLN1-AS1 | ENST00000524818.1 | n.27G>C | non_coding_transcript_exon_variant | 1/2 | 2 | |||||
UBQLN1 | ENST00000529923.1 | c.-19C>G | upstream_gene_variant | 2 | ENSP00000434194.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152164Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000105 AC: 15AN: 1431550Hom.: 0 Cov.: 31 AF XY: 0.00000986 AC XY: 7AN XY: 709932
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GnomAD4 genome AF: 0.0000328 AC: 5AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74464
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Mar 28, 2018 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at