chr20-1313450-C-G
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_080489.5(SDCBP2):āc.274G>Cā(p.Gly92Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000136 in 1,600,518 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00014 ( 0 hom., cov: 32)
Exomes š: 0.00014 ( 0 hom. )
Consequence
SDCBP2
NM_080489.5 missense
NM_080489.5 missense
Scores
3
9
6
Clinical Significance
Conservation
PhyloP100: 5.49
Genes affected
SDCBP2 (HGNC:15756): (syndecan binding protein 2) The protein encoded by this gene contains two class II PDZ domains. PDZ domains facilitate protein-protein interactions by binding to the cytoplasmic C-terminus of transmembrane proteins, and PDZ-containing proteins mediate cell signaling and the organization of protein complexes. The encoded protein binds to phosphatidylinositol 4, 5-bisphosphate (PIP2) and plays a role in nuclear PIP2 organization and cell division. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. Read-through transcription also exists between this gene and the upstream FKBP1A (FK506 binding protein 1A, 12kDa) gene, as represented in GeneID:100528031. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.854
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDCBP2 | NM_080489.5 | c.274G>C | p.Gly92Arg | missense_variant | 5/9 | ENST00000360779.4 | |
FKBP1A-SDCBP2 | NR_037661.1 | n.552G>C | non_coding_transcript_exon_variant | 6/10 | |||
SDCBP2 | NM_001199784.2 | c.274G>C | p.Gly92Arg | missense_variant | 5/9 | ||
SDCBP2 | NM_015685.6 | c.19G>C | p.Gly7Arg | missense_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDCBP2 | ENST00000360779.4 | c.274G>C | p.Gly92Arg | missense_variant | 5/9 | 1 | NM_080489.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152222Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000579 AC: 13AN: 224350Hom.: 0 AF XY: 0.0000654 AC XY: 8AN XY: 122268
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GnomAD4 exome AF: 0.000135 AC: 196AN: 1448296Hom.: 0 Cov.: 31 AF XY: 0.000138 AC XY: 99AN XY: 719726
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GnomAD4 genome AF: 0.000138 AC: 21AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74368
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2023 | The c.274G>C (p.G92R) alteration is located in exon 5 (coding exon 4) of the SDCBP2 gene. This alteration results from a G to C substitution at nucleotide position 274, causing the glycine (G) at amino acid position 92 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
M_CAP
Benign
D
MetaRNN
Pathogenic
D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M;.;M;M
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D;D
REVEL
Uncertain
Sift
Uncertain
D;D;D;D
Sift4G
Uncertain
D;D;D;D
Polyphen
D;.;D;D
Vest4
MutPred
Gain of MoRF binding (P = 0.0073);.;Gain of MoRF binding (P = 0.0073);Gain of MoRF binding (P = 0.0073);
MVP
MPC
0.70
ClinPred
D
GERP RS
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at