rs150432878

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_152699.5(SENP5):​c.356T>A​(p.Leu119Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L119P) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

SENP5
NM_152699.5 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.32
Variant links:
Genes affected
SENP5 (HGNC:28407): (SUMO specific peptidase 5) The reversible posttranslational modification of proteins by the addition of small ubiquitin-like SUMO proteins (see SUMO1; MIM 601912) is required for numerous biologic processes. SUMO-specific proteases, such as SENP5, are responsible for the initial processing of SUMO precursors to generate a C-terminal diglycine motif required for the conjugation reaction. They also have isopeptidase activity for the removal of SUMO from high molecular mass SUMO conjugates (Di Bacco et al., 2006 [PubMed 16738315]).[supplied by OMIM, Jun 2009]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.13788179).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SENP5NM_152699.5 linkc.356T>A p.Leu119Gln missense_variant Exon 2 of 10 ENST00000323460.10 NP_689912.2 Q96HI0-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SENP5ENST00000323460.10 linkc.356T>A p.Leu119Gln missense_variant Exon 2 of 10 1 NM_152699.5 ENSP00000327197.5 Q96HI0-1
SENP5ENST00000445299.6 linkc.356T>A p.Leu119Gln missense_variant Exon 2 of 9 2 ENSP00000390231.2 Q96HI0-2
SENP5ENST00000419026.5 linkc.-17-14129T>A intron_variant Intron 1 of 8 3 ENSP00000396927.1 C9JHT8

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.083
BayesDel_addAF
Benign
-0.089
T
BayesDel_noAF
Benign
-0.37
CADD
Benign
13
DANN
Uncertain
0.99
DEOGEN2
Benign
0.021
.;T
Eigen
Benign
-0.074
Eigen_PC
Benign
-0.016
FATHMM_MKL
Benign
0.74
D
LIST_S2
Benign
0.84
T;T
M_CAP
Benign
0.024
T
MetaRNN
Benign
0.14
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.90
L;L
PrimateAI
Benign
0.35
T
PROVEAN
Benign
-0.25
N;N
REVEL
Benign
0.082
Sift
Uncertain
0.0010
D;D
Sift4G
Benign
0.091
T;T
Polyphen
0.14
.;B
Vest4
0.37
MutPred
0.24
Gain of solvent accessibility (P = 0.0374);Gain of solvent accessibility (P = 0.0374);
MVP
0.10
MPC
0.32
ClinPred
0.57
D
GERP RS
5.2
Varity_R
0.38
gMVP
0.19

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-196612408; API