17-29630976-TC-CT

Variant names:

• chr17-29630976-TC-CT
• NM_001282129.2:c.4217_4218delGAinsAG
• SSH2 p.Gly1406Glu

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001282129.2(SSH2):​c.4217_4218delGAinsAG​(p.Gly1406Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SSH2 NM_001282129.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.405
• Publications: 0 publications found

Genes affected

SSH2 (HGNC:30580): (slingshot protein phosphatase 2) This gene encodes a protein tyrosine phosphatase that plays a key role in the regulation of actin filaments. The encoded protein dephosphorylates and activates cofilin, which promotes actin filament depolymerization. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

ABHD15-AS1 (HGNC:49685): (ABHD15 antisense RNA 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001282129.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSH2	NM_001282129.2	MANE Select	c.4217_4218delGAinsAG	p.Gly1406Glu	missense	N/A	NP_001269058.1	F5H527
	SSH2	NM_033389.3		c.4136_4137delGAinsAG	p.Gly1379Glu	missense	N/A	NP_203747.2	Q76I76-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSH2	ENST00000540801.6	TSL:2 MANE Select	c.4217_4218delGAinsAG	p.Gly1406Glu	missense	N/A	ENSP00000444743.1	F5H527
	SSH2	ENST00000269033.7	TSL:1	c.4136_4137delGAinsAG	p.Gly1379Glu	missense	N/A	ENSP00000269033.3	Q76I76-1
	SSH2	ENST00000649863.1		c.4154_4155delGAinsAG	p.Gly1385Glu	missense	N/A	ENSP00000497148.1	A0A3B3IS79

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.41

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr17-27957994;