12-10213215-T-A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_031412.4(GABARAPL1):c.86T>A(p.Val29Asp) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
GABARAPL1
NM_031412.4 missense
NM_031412.4 missense
Scores
12
3
2
Clinical Significance
Conservation
PhyloP100: 4.81
Publications
0 publications found
Genes affected
GABARAPL1 (HGNC:4068): (GABA type A receptor associated protein like 1) Enables Tat protein binding activity and ubiquitin protein ligase binding activity. Predicted to be involved in autophagosome assembly; autophagy of mitochondrion; and cellular response to nitrogen starvation. Located in autophagosome. Colocalizes with mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.915
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_031412.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| GABARAPL1 | TSL:1 MANE Select | c.86T>A | p.Val29Asp | missense | Exon 1 of 4 | ENSP00000266458.5 | Q9H0R8-1 | ||
| GABARAPL1 | TSL:2 | c.86T>A | p.Val29Asp | missense | Exon 1 of 3 | ENSP00000411256.2 | Q9H0R8-2 | ||
| GABARAPL1 | TSL:5 | c.86T>A | p.Val29Asp | missense | Exon 2 of 4 | ENSP00000445857.1 | Q9H0R8-2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1307528Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 650218
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
1307528
Hom.:
Cov.:
27
AF XY:
AC XY:
0
AN XY:
650218
African (AFR)
AF:
AC:
0
AN:
30346
American (AMR)
AF:
AC:
0
AN:
35452
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
23232
East Asian (EAS)
AF:
AC:
0
AN:
34902
South Asian (SAS)
AF:
AC:
0
AN:
79044
European-Finnish (FIN)
AF:
AC:
0
AN:
43352
Middle Eastern (MID)
AF:
AC:
0
AN:
5354
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1002270
Other (OTH)
AF:
AC:
0
AN:
53576
GnomAD4 genome
GnomAD4 genome
Cov.:
31
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
DANN
Benign
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D
MetaSVM
Uncertain
T
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D
REVEL
Pathogenic
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MutPred
Loss of MoRF binding (P = 0.011)
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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