3-39098745-CC-TT

Variant names:

• chr3-39098745-CC-TT
• NM_031899.4:c.1064_1065delGGinsAA
• GORASP1 p.Arg355Gln

Variant summary

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

The NM_031899.4(GORASP1):​c.1064_1065delGGinsAA​(p.Arg355Gln) 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R355W) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: GORASP1 NM_031899.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 0 publications found

Genes affected

GORASP1 (HGNC:16769): (golgi reassembly stacking protein 1) The Golgi complex plays a key role in the sorting and modification of proteins exported from the endoplasmic reticulum. The protein encoded by this gene is a membrane protein involved in establishing the stacked structure of the Golgi apparatus. It is a caspase-3 substrate, and cleavage of this encoded protein contributes to Golgi fragmentation in apoptosis. This encoded protein can form a complex with the Golgi matrix protein GOLGA2, and this complex binds to the vesicle docking protein p115. Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, Jul 2013]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031899.4. 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
	GORASP1	NM_031899.4	MANE Select	c.1064_1065delGGinsAA	p.Arg355Gln	missense	N/A	NP_114105.1	Q9BQQ3-1
	GORASP1	NM_001410726.1		c.974_975delGGinsAA	p.Arg325Gln	missense	N/A	NP_001397655.1	A0A8Q3SHU6
	GORASP1	NM_001410731.1		c.884_885delGGinsAA	p.Arg295Gln	missense	N/A	NP_001397660.1	A0A8Q3WL08

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GORASP1	ENST00000319283.8	TSL:1 MANE Select	c.1064_1065delGGinsAA	p.Arg355Gln	missense	N/A	ENSP00000313869.3	Q9BQQ3-1
	GORASP1	ENST00000452389.7	TSL:1	n.*375_*376delGGinsAA		non_coding_transcript_exon	Exon 8 of 9	ENSP00000403167.2	Q9BQQ3-2
	GORASP1	ENST00000453680.6	TSL:1	n.*64_*65delGGinsAA		non_coding_transcript_exon	Exon 8 of 9	ENSP00000392020.1	G3V0G1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.2

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: chr3-39140236;