16-58718560-ACC-GCT

Variant names:

• chr16-58718560-ACC-GCT
• NM_002080.4:c.562_564delGGTinsAGC
• GOT2 p.Gly188Ser

Variant summary

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

The NM_002080.4(GOT2):​c.562_564delGGTinsAGC​(p.Gly188Ser) variant causes a missense change. 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 Benign in ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: GOT2 NM_002080.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.04
• Publications: 0 publications found

Genes affected

GOT2 (HGNC:4433): (glutamic-oxaloacetic transaminase 2) Glutamic-oxaloacetic transaminase is a pyridoxal phosphate-dependent enzyme which exists in cytoplasmic and inner-membrane mitochondrial forms, GOT1 and GOT2, respectively. GOT plays a role in amino acid metabolism and the urea and tricarboxylic acid cycles. The two enzymes are homodimeric and show close homology. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2013]

GOT2 Gene-Disease associations (from GenCC):

• developmental and epileptic encephalopathy, 82

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002080.4. 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
	GOT2	NM_002080.4	MANE Select	c.562_564delGGTinsAGC	p.Gly188Ser	missense	N/A	NP_002071.2	P00505-1
	GOT2	NM_001286220.2		c.433_435delGGTinsAGC	p.Gly145Ser	missense	N/A	NP_001273149.1	P00505-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOT2	ENST00000245206.10	TSL:1 MANE Select	c.562_564delGGTinsAGC	p.Gly188Ser	missense	N/A	ENSP00000245206.5	P00505-1
	GOT2	ENST00000954610.1		c.562_564delGGTinsAGC	p.Gly188Ser	missense	N/A	ENSP00000624669.1
	GOT2	ENST00000857880.1		c.562_564delGGTinsAGC	p.Gly188Ser	missense	N/A	ENSP00000527939.1

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		6.0

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: chr16-58752464;