rs760378079

Variant names:

• chr15-44668359-C-A
• NM_001387263.1:c.1348G>T

Your query was ambiguous. Multiple possible variants found:

• chr15-44668359-C-A
• chr15-44668359-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001387263.1(PATL2):​c.1348G>T​(p.Val450Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000715 in 1,398,622 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.1e-7 (0 hom.)
• Consequence: PATL2 NM_001387263.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.520

Genes affected

PATL2 (HGNC:33630): (PAT1 homolog 2) Predicted to enable RNA binding activity. Predicted to be involved in P-body assembly and deadenylation-dependent decapping of nuclear-transcribed mRNA. Predicted to act upstream of or within negative regulation of cytoplasmic mRNA processing body assembly. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.07066986).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PATL2	NM_001387263.1	c.1348G>T	p.Val450Leu	missense_variant	Exon 15 of 18	ENST00000682850.1	NP_001374192.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PATL2	ENST00000682850.1	c.1348G>T	p.Val450Leu	missense_variant	Exon 15 of 18		NM_001387263.1	ENSP00000508024.1
PATL2	ENST00000434130.6	c.1348G>T	p.Val450Leu	missense_variant	Exon 13 of 16	5		ENSP00000416673.1
PATL2	ENST00000560780.1	c.781G>T	p.Val261Leu	missense_variant	Exon 12 of 15	2		ENSP00000453695.1
PATL2	ENST00000558809.1	c.127G>T	p.Val43Leu	missense_variant	Exon 1 of 3	3		ENSP00000453723.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.15e-7 AC: 1 AN: 1398622 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 689818

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.27e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.58
CADD	Benign	5.9
DANN	Benign	0.81
DEOGEN2	Benign	0.0039	T;T;.;.
Eigen	Benign	-0.95
Eigen_PC	Benign	-0.90
FATHMM_MKL	Benign	0.14	N
LIST_S2	Benign	0.64	.;T;T;T
M_CAP	Benign	0.0064	T
MetaRNN	Benign	0.071	T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.2	L;L;.;.
PrimateAI	Benign	0.40	T
PROVEAN	Benign	-0.46	N;N;N;N
REVEL	Benign	0.084
Sift	Benign	0.50	T;T;T;T
Sift4G	Benign	1.0	T;T;T;T
Polyphen		0.0090	B;B;.;.
Vest4		0.094
MutPred		0.52		Gain of helix (P = 0.062);Gain of helix (P = 0.062);.;.;
MVP		0.048
MPC		.;3.61486425784E-4;.;.
ClinPred		0.034	T
GERP RS		1.1
Varity_R		0.039
gMVP		0.082

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		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: chr15-44960557;