chr17-73338649-G-C

Variant names:

• chr17-73338649-G-C
• NM_001144952.2:c.6457C>G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001144952.2(SDK2):​c.6457C>G​(p.Pro2153Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00000215 in 1,396,200 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: SDK2 NM_001144952.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.10

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.41825876).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SDK2	NM_001144952.2	c.6457C>G	p.Pro2153Ala	missense_variant	Exon 45 of 45	ENST00000392650.8	NP_001138424.1
SDK2	XM_011524914.3	c.6400C>G	p.Pro2134Ala	missense_variant	Exon 44 of 44		XP_011523216.1
SDK2	XM_011524915.3	c.6322+135C>G		intron_variant	Intron 45 of 45		XP_011523217.1
SDK2	XM_047436313.1	c.6265+135C>G		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.6457C>G	p.Pro2153Ala	missense_variant	Exon 45 of 45	5	NM_001144952.2	ENSP00000376421.3
SDK2	ENST00000424778.1	c.3928C>G	p.Pro1310Ala	missense_variant	Exon 27 of 27	5		ENSP00000407098.1
SDK2	ENST00000410094.5	n.1530C>G		non_coding_transcript_exon_variant	Exon 10 of 10	5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000215 AC: 3 AN: 1396200 Hom.: 0 Cov.: 31 AF XY: 0.00000436 AC XY: 3 AN XY: 688308

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

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: 0.0000521

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Nov 08, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.6457C>G (p.P2153A) alteration is located in exon 45 (coding exon 45) of the SDK2 gene. This alteration results from a C to G substitution at nucleotide position 6457, causing the proline (P) at amino acid position 2153 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.16
BayesDel_addAF	Uncertain	0.040	T
BayesDel_noAF	Benign	-0.18
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.041	T;T
Eigen	Uncertain	0.37
Eigen_PC	Uncertain	0.45
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.85	T;T
M_CAP	Uncertain	0.095	D
MetaRNN	Benign	0.42	T;T
MetaSVM	Benign	-0.61	T
MutationAssessor	Uncertain	2.2	M;.
PrimateAI	Uncertain	0.70	T
PROVEAN	Benign	-1.3	N;N
REVEL	Benign	0.25
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0	D;D
Polyphen		0.87	P;.
Vest4		0.41
MutPred		0.46		Loss of glycosylation at P2153 (P = 0.0122);.;
MVP		0.79
MPC		0.87
ClinPred		0.97	D
GERP RS		4.8
Varity_R		0.36
gMVP		0.25

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: chr17-71334788;