chr17-73338723-C-G
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001144952.2(SDK2):āc.6383G>Cā(p.Arg2128Pro) variant causes a missense change. The variant allele was found at a frequency of 0.000000685 in 1,460,558 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes š: 6.8e-7 ( 0 hom. )
Consequence
SDK2
NM_001144952.2 missense
NM_001144952.2 missense
Scores
3
7
9
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.64
Genes affected
SDK2 (HGNC:19308): (sidekick cell adhesion molecule 2) The protein encoded by this gene is a member of the immunoglobulin superfamily. The protein contains two immunoglobulin domains and thirteen fibronectin type III domains. Fibronectin type III domains are present in both extracellular and intracellular proteins and tandem repeats are known to contain binding sites for DNA, heparin and the cell surface. This protein, and a homologous mouse sequence, are very similar to the Drosophila sidekick gene product but the specific function of this superfamily member is not yet known. Evidence for alternative splicing at this gene locus has been observed but the full-length nature of additional variants has not yet been determined. [provided by RefSeq, Jul 2008]
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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 |
---|---|---|---|---|---|---|---|---|
SDK2 | NM_001144952.2 | c.6383G>C | p.Arg2128Pro | missense_variant | Exon 45 of 45 | ENST00000392650.8 | NP_001138424.1 | |
SDK2 | XM_011524914.3 | c.6326G>C | p.Arg2109Pro | missense_variant | Exon 44 of 44 | XP_011523216.1 | ||
SDK2 | XM_011524915.3 | c.6322+61G>C | intron_variant | Intron 45 of 45 | XP_011523217.1 | |||
SDK2 | XM_047436313.1 | c.6265+61G>C | intron_variant | Intron 44 of 44 | XP_047292269.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SDK2 | ENST00000392650.8 | c.6383G>C | p.Arg2128Pro | missense_variant | Exon 45 of 45 | 5 | NM_001144952.2 | ENSP00000376421.3 | ||
SDK2 | ENST00000424778.1 | c.3854G>C | p.Arg1285Pro | missense_variant | Exon 27 of 27 | 5 | ENSP00000407098.1 | |||
SDK2 | ENST00000410094.5 | n.1456G>C | non_coding_transcript_exon_variant | Exon 10 of 10 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460558Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 726520
GnomAD4 exome
AF:
AC:
1
AN:
1460558
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
726520
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
D
MetaRNN
Uncertain
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
D;.
Vest4
MutPred
Loss of MoRF binding (P = 0.0128);.;
MVP
MPC
ClinPred
D
GERP RS
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
Publications
No publications associated with this variant yet.