2-109129578-C-G

Variant summary

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

The NM_001099289.3(SH3RF3):​c.38C>G​(p.Ala13Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000003 in 1,332,432 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 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. A13V) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 34)
Exomes š‘“: 0.0000030 ( 0 hom. )

Consequence

SH3RF3
NM_001099289.3 missense

Scores

2
1
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.64
Variant links:
Genes affected
SH3RF3 (HGNC:24699): (SH3 domain containing ring finger 3) Enables ubiquitin protein ligase activity. Involved in positive regulation of JNK cascade and protein autoubiquitination. [provided by Alliance of Genome Resources, Apr 2022]
RANBP2 (HGNC:9848): (RAN binding protein 2) RAN is a small GTP-binding protein of the RAS superfamily that is associated with the nuclear membrane and is thought to control a variety of cellular functions through its interactions with other proteins. This gene encodes a very large RAN-binding protein that immunolocalizes to the nuclear pore complex. The protein is a giant scaffold and mosaic cyclophilin-related nucleoporin implicated in the Ran-GTPase cycle. The encoded protein directly interacts with the E2 enzyme UBC9 and strongly enhances SUMO1 transfer from UBC9 to the SUMO1 target SP100. These findings place sumoylation at the cytoplasmic filaments of the nuclear pore complex and suggest that, for some substrates, modification and nuclear import are linked events. This gene is partially duplicated in a gene cluster that lies in a hot spot for recombination on chromosome 2q. [provided by RefSeq, Jul 2008]
SH3RF3-AS1 (HGNC:44168): (SH3RF3 antisense RNA 1)

Genome browser will be placed here

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=0.15285888).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SH3RF3NM_001099289.3 linkc.38C>G p.Ala13Gly missense_variant Exon 1 of 10 ENST00000309415.8 NP_001092759.1 Q8TEJ3
SH3RF3XM_011511109.3 linkc.38C>G p.Ala13Gly missense_variant Exon 1 of 9 XP_011509411.1
RANBP2XM_047445367.1 linkc.8370+356532C>G intron_variant Intron 24 of 24 XP_047301323.1
SH3RF3-AS1NR_029193.1 linkn.542G>C non_coding_transcript_exon_variant Exon 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SH3RF3ENST00000309415.8 linkc.38C>G p.Ala13Gly missense_variant Exon 1 of 10 5 NM_001099289.3 ENSP00000309186.6 Q8TEJ3

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD3 exomes
AF:
0.0000360
AC:
3
AN:
83376
Hom.:
0
AF XY:
0.0000211
AC XY:
1
AN XY:
47480
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000192
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000300
AC:
4
AN:
1332432
Hom.:
0
Cov.:
32
AF XY:
0.00000152
AC XY:
1
AN XY:
656868
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000143
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
34
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Benign
-0.40
T
BayesDel_noAF
Benign
-0.53
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.0014
T
Eigen
Benign
-0.087
Eigen_PC
Benign
-0.086
FATHMM_MKL
Benign
0.63
D
LIST_S2
Benign
0.48
T
M_CAP
Pathogenic
0.64
D
MetaRNN
Benign
0.15
T
MetaSVM
Benign
-1.0
T
PrimateAI
Pathogenic
0.85
D
PROVEAN
Benign
-0.080
N
REVEL
Benign
0.035
Sift
Benign
0.17
T
Sift4G
Benign
0.30
T
Polyphen
0.70
P
Vest4
0.14
MutPred
0.25
Gain of glycosylation at K12 (P = 0.0933);
MVP
0.32
MPC
0.20
ClinPred
0.22
T
GERP RS
2.3
Varity_R
0.099
gMVP
0.34

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1024924304; hg19: chr2-109746034; API