15-44668467-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001387263.1(PATL2):āc.1240T>Cā(p.Phe414Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000445 in 1,551,094 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000026 ( 0 hom., cov: 32)
Exomes š: 0.000046 ( 0 hom. )
Consequence
PATL2
NM_001387263.1 missense
NM_001387263.1 missense
Scores
1
4
14
Clinical Significance
Conservation
PhyloP100: 3.40
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PATL2 | NM_001387263.1 | c.1240T>C | p.Phe414Leu | missense_variant | 15/18 | ENST00000682850.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PATL2 | ENST00000682850.1 | c.1240T>C | p.Phe414Leu | missense_variant | 15/18 | NM_001387263.1 | A2 | ||
PATL2 | ENST00000434130.6 | c.1240T>C | p.Phe414Leu | missense_variant | 13/16 | 5 | A2 | ||
PATL2 | ENST00000560780.1 | c.673T>C | p.Phe225Leu | missense_variant | 12/15 | 2 | P2 | ||
PATL2 | ENST00000558809.1 | c.19T>C | p.Phe7Leu | missense_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152180Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000390 AC: 6AN: 153700Hom.: 0 AF XY: 0.0000368 AC XY: 3AN XY: 81570
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GnomAD4 exome AF: 0.0000465 AC: 65AN: 1398914Hom.: 0 Cov.: 30 AF XY: 0.0000435 AC XY: 30AN XY: 689986
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74354
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2024 | The c.1240T>C (p.F414L) alteration is located in exon 13 (coding exon 12) of the PATL2 gene. This alteration results from a T to C substitution at nucleotide position 1240, causing the phenylalanine (F) at amino acid position 414 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
.;T;T;T
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;.;.
MutationTaster
Benign
D;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;D;N
REVEL
Benign
Sift
Benign
T;T;D;T
Sift4G
Benign
T;T;D;T
Polyphen
D;D;.;.
Vest4
MutPred
Loss of methylation at K415 (P = 0.0273);Loss of methylation at K415 (P = 0.0273);.;.;
MVP
MPC
.;3.40522473235E-4;.;.
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at