NM_001099666.2:c.877G>A

Variant names:

• chr9-69723396-C-T
• NM_001099666.2:c.877G>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001099666.2(PTAR1):​c.877G>A​(p.Glu293Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: PTAR1 NM_001099666.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.33
• Publications: 0 publications found

Genes affected

PTAR1 (HGNC:30449): (protein prenyltransferase alpha subunit repeat containing 1) Predicted to enable protein prenyltransferase activity. Predicted to be involved in protein prenylation. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2023176).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001099666.2. 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
	PTAR1	NM_001099666.2	MANE Select	c.877G>A	p.Glu293Lys	missense	Exon 6 of 8	NP_001093136.1	Q7Z6K3
	PTAR1	NM_001366936.1		c.877G>A	p.Glu293Lys	missense	Exon 6 of 7	NP_001353865.1
	PTAR1	NM_001366937.1		c.877G>A	p.Glu293Lys	missense	Exon 6 of 8	NP_001353866.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTAR1	ENST00000340434.5	TSL:1 MANE Select	c.877G>A	p.Glu293Lys	missense	Exon 6 of 8	ENSP00000344299.4	Q7Z6K3
	PTAR1	ENST00000377200.9	TSL:1	c.640G>A	p.Glu214Lys	missense	Exon 4 of 5	ENSP00000366405.5	X6R9N0
	PTAR1	ENST00000912951.1		c.640G>A	p.Glu214Lys	missense	Exon 4 of 6	ENSP00000583010.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.087
BayesDel_addAF	Benign	-0.097	T
BayesDel_noAF	Benign	-0.38
CADD	Benign	21
DANN	Benign	0.95
DEOGEN2	Benign	0.010	T
Eigen	Uncertain	0.30
Eigen_PC	Uncertain	0.43
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Uncertain	0.89	D
M_CAP	Benign	0.0065	T
MetaRNN	Benign	0.20	T
MetaSVM	Benign	-0.88	T
MutationAssessor	Benign	1.6	L
PhyloP100		2.3
PrimateAI	Benign	0.46	T
PROVEAN	Benign	-1.2	N
REVEL	Benign	0.11
Sift	Benign	0.35	T
Sift4G	Benign	0.20	T
Polyphen		0.0030	B
Vest4		0.32
MutPred		0.51		Gain of methylation at E293 (P = 0.0189)
MVP		0.15
MPC		0.35
ClinPred		0.32	T
GERP RS		6.0
PromoterAI		-0.021	Neutral
Varity_R		0.18
gMVP		0.24
Mutation Taster		=56/44	polymorphism

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

Other links and lift over

hg19: chr9-72338312;