1-156244264-GG-CC

Variant names:

• chr1-156244264-GG-CC
• NM_198406.3:c.899_900delCCinsGG
• PAQR6 p.Ala300Gly

Variant summary

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

The NM_198406.3(PAQR6):​c.899_900delCCinsGG​(p.Ala300Gly) 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. A300V) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: PAQR6 NM_198406.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40
• Publications: 0 publications found

Genes affected

PAQR6 (HGNC:30132): (progestin and adipoQ receptor family member 6) Predicted to enable signaling receptor activity. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198406.3. 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
	PAQR6	NM_198406.3	MANE Select	c.899_900delCCinsGG	p.Ala300Gly	missense	N/A	NP_940798.1	Q5TCK7
	PAQR6	NM_024897.4		c.652_653delCCinsGG	p.Pro218Gly	missense	N/A	NP_079173.2
	PAQR6	NM_001272104.2		c.899_900delCCinsGG	p.Ala300Gly	missense	N/A	NP_001259033.1	Q5TCK7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAQR6	ENST00000292291.10	TSL:1 MANE Select	c.899_900delCCinsGG	p.Ala300Gly	missense	N/A	ENSP00000292291.5	Q6TCH4-1
	PAQR6	ENST00000368270.2	TSL:1	c.827_828delCCinsGG	p.Ala276Gly	missense	N/A	ENSP00000357253.1	Q6TCH4-4
	PAQR6	ENST00000623241.3	TSL:1	c.232_233delCCinsGG	p.Pro78Gly	missense	N/A	ENSP00000485607.1	Q7Z4Q8

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		1.4

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: chr1-156214055;