4-168878161-CCCGCCA-C
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP3
The ENST00000507735.6(PALLD):c.273_278delGCCACC(p.Pro92_Pro93del) variant causes a disruptive inframe deletion change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. P91P) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 29)
Exomes 𝑓: 0.0000015 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PALLD
ENST00000507735.6 disruptive_inframe_deletion
ENST00000507735.6 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.05
Publications
0 publications found
Genes affected
PALLD (HGNC:17068): (palladin, cytoskeletal associated protein) This gene encodes a cytoskeletal protein that is required for organizing the actin cytoskeleton. The protein is a component of actin-containing microfilaments, and it is involved in the control of cell shape, adhesion, and contraction. Polymorphisms in this gene are associated with a susceptibility to pancreatic cancer type 1, and also with a risk for myocardial infarction. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
CBR4 (HGNC:25891): (carbonyl reductase 4) Enables several functions, including 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity; NADPH binding activity; and NADPH dehydrogenase (quinone) activity. Involved in fatty acid biosynthetic process; glycoside metabolic process; and protein tetramerization. Located in mitochondrial matrix. Part of oxidoreductase complex. [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 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP3
Nonframeshift variant in repetitive region in ENST00000507735.6
Variant Effect in Transcripts
ACMG analysis was done for transcript: ENST00000507735.6. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PALLD | NM_001166108.2 | MANE Select | c.1965-12758_1965-12753delGCCACC | intron | N/A | NP_001159580.1 | |||
| PALLD | NM_001166110.2 | c.273_278delGCCACC | p.Pro92_Pro93del | disruptive_inframe_deletion | Exon 2 of 12 | NP_001159582.1 | |||
| PALLD | NM_016081.4 | c.1965-12758_1965-12753delGCCACC | intron | N/A | NP_057165.3 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PALLD | ENST00000507735.6 | TSL:1 | c.273_278delGCCACC | p.Pro92_Pro93del | disruptive_inframe_deletion | Exon 2 of 12 | ENSP00000424016.1 | ||
| PALLD | ENST00000505667.6 | TSL:1 MANE Select | c.1965-12758_1965-12753delGCCACC | intron | N/A | ENSP00000425556.1 | |||
| PALLD | ENST00000261509.10 | TSL:1 | c.1965-12758_1965-12753delGCCACC | intron | N/A | ENSP00000261509.6 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
29
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000149 AC: 2AN: 1339820Hom.: 0 AF XY: 0.00000151 AC XY: 1AN XY: 660412 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
2
AN:
1339820
Hom.:
AF XY:
AC XY:
1
AN XY:
660412
show subpopulations
African (AFR)
AF:
AC:
0
AN:
27192
American (AMR)
AF:
AC:
0
AN:
30558
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
23756
East Asian (EAS)
AF:
AC:
0
AN:
30872
South Asian (SAS)
AF:
AC:
0
AN:
74818
European-Finnish (FIN)
AF:
AC:
0
AN:
33196
Middle Eastern (MID)
AF:
AC:
0
AN:
4054
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1059664
Other (OTH)
AF:
AC:
0
AN:
55710
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.550
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
29
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions as Germline
Significance:Uncertain significance
Revision:criteria provided, multiple submitters, no conflicts
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
-
1
-
Pancreatic adenocarcinoma (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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