chr15-44668433-G-A
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001387263.1(PATL2):c.1274C>T(p.Thr425Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000214 in 1,399,062 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
PATL2
NM_001387263.1 missense
NM_001387263.1 missense
Scores
1
10
8
Clinical Significance
Conservation
PhyloP100: 5.27
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.1274C>T | p.Thr425Ile | missense_variant | 15/18 | ENST00000682850.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PATL2 | ENST00000682850.1 | c.1274C>T | p.Thr425Ile | missense_variant | 15/18 | NM_001387263.1 | A2 | ||
PATL2 | ENST00000434130.6 | c.1274C>T | p.Thr425Ile | missense_variant | 13/16 | 5 | A2 | ||
PATL2 | ENST00000560780.1 | c.707C>T | p.Thr236Ile | missense_variant | 12/15 | 2 | P2 | ||
PATL2 | ENST00000558809.1 | c.53C>T | p.Thr18Ile | missense_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000650 AC: 1AN: 153940Hom.: 0 AF XY: 0.0000122 AC XY: 1AN XY: 81692
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GnomAD4 exome AF: 0.00000214 AC: 3AN: 1399062Hom.: 0 Cov.: 30 AF XY: 0.00000290 AC XY: 2AN XY: 690050
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
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 | Dec 20, 2023 | The c.1274C>T (p.T425I) alteration is located in exon 13 (coding exon 12) of the PATL2 gene. This alteration results from a C to T substitution at nucleotide position 1274, causing the threonine (T) at amino acid position 425 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
.;T;T;T
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.;.
MutationTaster
Benign
D;N;N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;D
REVEL
Benign
Sift
Uncertain
D;D;D;D
Sift4G
Uncertain
D;D;D;D
Polyphen
P;P;.;.
Vest4
MutPred
Gain of helix (P = 0.0496);Gain of helix (P = 0.0496);.;.;
MVP
MPC
.;3.40522473235E-4;.;.
ClinPred
D
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