17-42852620-GT-CA

Variant names:

• chr17-42852620-GT-CA
• NM_003734.4:c.1277_1278delGTinsCA
• AOC3 p.Arg426Pro

Variant summary

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

The NM_003734.4(AOC3):​c.1277_1278delGTinsCA​(p.Arg426Pro) 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. R426C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: AOC3 NM_003734.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367
• Publications: 0 publications found

Genes affected

AOC3 (HGNC:550): (amine oxidase copper containing 3) This gene encodes a member of the semicarbazide-sensitive amine oxidase family. Copper amine oxidases catalyze the oxidative conversion of amines to aldehydes in the presence of copper and quinone cofactor. The encoded protein is localized to the cell surface, has adhesive properties as well as monoamine oxidase activity, and may be involved in leukocyte trafficking. Alterations in levels of the encoded protein may be associated with many diseases, including diabetes mellitus. A pseudogene of this gene has been described and is located approximately 9-kb downstream on the same chromosome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2013]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003734.4. 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
	AOC3	NM_003734.4	MANE Select	c.1277_1278delGTinsCA	p.Arg426Pro	missense	N/A	NP_003725.1	Q16853-1
	AOC3	NM_001277731.2		c.1277_1278delGTinsCA	p.Arg426Pro	missense	N/A	NP_001264660.1	Q16853-2
	AOC3	NR_102422.2		n.1422_1423delGTinsCA		non_coding_transcript_exon	Exon 1 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AOC3	ENST00000308423.7	TSL:1 MANE Select	c.1277_1278delGTinsCA	p.Arg426Pro	missense	N/A	ENSP00000312326.1	Q16853-1
	AOC3	ENST00000613571.1	TSL:1	c.1277_1278delGTinsCA	p.Arg426Pro	missense	N/A	ENSP00000484312.1	Q16853-2
	AOC3	ENST00000587330.1	TSL:5	n.-134_-133delGTinsCA		upstream_gene	N/A	ENSP00000464787.1	K7EIK5

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		-0.37

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: chr17-41004637;