rs375709871
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_005500.3(SAE1):c.257C>G(p.Ser86Cys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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. S86F) has been classified as Uncertain significance.
Frequency
Genomes: not found (cov: 32)
Consequence
SAE1
NM_005500.3 missense
NM_005500.3 missense
Scores
1
6
12
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.80
Genes affected
SAE1 (HGNC:30660): (SUMO1 activating enzyme subunit 1) Posttranslational modification of proteins by the addition of the small protein SUMO (see SUMO1; MIM 601912), or sumoylation, regulates protein structure and intracellular localization. SAE1 and UBA2 (MIM 613295) form a heterodimer that functions as a SUMO-activating enzyme for the sumoylation of proteins (Okuma et al., 1999 [PubMed 9920803]).[supplied by OMIM, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SAE1 | NM_005500.3 | c.257C>G | p.Ser86Cys | missense_variant | Exon 3 of 9 | ENST00000270225.12 | NP_005491.1 | |
SAE1 | NM_001145713.2 | c.257C>G | p.Ser86Cys | missense_variant | Exon 3 of 7 | NP_001139185.1 | ||
SAE1 | NM_001145714.2 | c.257C>G | p.Ser86Cys | missense_variant | Exon 3 of 8 | NP_001139186.1 | ||
SAE1 | NR_027280.2 | n.437C>G | non_coding_transcript_exon_variant | Exon 3 of 9 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;.;.;.;T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T;T;T;T;T;T;T
M_CAP
Benign
T
MetaRNN
Uncertain
T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;.;.;L;.;.;L;L
PrimateAI
Uncertain
T
PROVEAN
Uncertain
.;.;.;D;.;.;D;D
REVEL
Benign
Sift
Uncertain
.;.;.;D;.;.;D;D
Sift4G
Uncertain
D;D;D;D;.;T;D;D
Polyphen
0.54
.;.;.;.;.;.;P;.
Vest4
0.40, 0.40, 0.41, 0.39
MutPred
0.61
.;.;.;Loss of disorder (P = 0.0224);.;Loss of disorder (P = 0.0224);Loss of disorder (P = 0.0224);Loss of disorder (P = 0.0224);
MVP
MPC
0.31
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at