chr2-60771544-C-G

Position:

• chr2-60771544-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_022894.4(PAPOLG):​c.518C>G​(p.Ala173Gly) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: PAPOLG NM_022894.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.04

Genes affected

PAPOLG (HGNC:14982): (poly(A) polymerase gamma) This gene encodes a member of the poly(A) polymerase family which catalyzes template-independent extension of the 3' end of a DNA/RNA strand. This enzyme shares 60% identity to the well characterized poly(A) polymerase II (PAPII) at the amino acid level. These two enzymes have similar organization of structural and functional domains. This enzyme is exclusively localized in the nucleus and exhibits both nonspecific and CPSF (cleavage and polyadenylation specificity factor)/AAUAAA-dependent polyadenylation activity. This gene is located on chromosome 2 in contrast to the PAPII gene, which is located on chromosome 14. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.3887021).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PAPOLG	NM_022894.4	c.518C>G	p.Ala173Gly	missense_variant	7/22	ENST00000238714.8	NP_075045.2
PAPOLG	XM_005264500.5	c.518C>G	p.Ala173Gly	missense_variant	7/21		XP_005264557.1
PAPOLG	XM_005264501.3	c.386C>G	p.Ala129Gly	missense_variant	7/22		XP_005264558.1
PAPOLG	XR_007080681.1	n.729C>G		non_coding_transcript_exon_variant	7/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PAPOLG	ENST00000238714.8	c.518C>G	p.Ala173Gly	missense_variant	7/22	1	NM_022894.4	ENSP00000238714	P1
PAPOLG	ENST00000414060.5	c.386C>G	p.Ala129Gly	missense_variant, NMD_transcript_variant	7/21	1		ENSP00000405599
PAPOLG	ENST00000453839.5	c.474+1033C>G		intron_variant, NMD_transcript_variant		1		ENSP00000414070
PAPOLG	ENST00000496283.5	n.572+1033C>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 23, 2023

The c.518C>G (p.A173G) alteration is located in exon 7 (coding exon 7) of the PAPOLG gene. This alteration results from a C to G substitution at nucleotide position 518, causing the alanine (A) at amino acid position 173 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.24
BayesDel_addAF	Uncertain	0.061	T
BayesDel_noAF	Benign	-0.15
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Benign	0.27	T
Eigen	Uncertain	0.28
Eigen_PC	Uncertain	0.42
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Uncertain	0.97	D
M_CAP	Benign	0.0062	T
MetaRNN	Benign	0.39	T
MetaSVM	Benign	-0.51	T
MutationAssessor	Uncertain	2.6	M
MutationTaster	Benign	1.0	D
PrimateAI	Uncertain	0.61	T
PROVEAN	Uncertain	-3.3	D
REVEL	Uncertain	0.29
Sift	Benign	0.030	D
Sift4G	Uncertain	0.042	D
Polyphen		0.015	B
Vest4		0.37
MutPred		0.71		Gain of sheet (P = 0.0344);
MVP		0.41
MPC		0.73
ClinPred		0.96	D
GERP RS		5.4
Varity_R		0.54
gMVP		0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-60998679;