3-18349584-TG-T
Variant names:
Variant summary
Our verdict is Likely pathogenic. The variant received 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_002971.6(SATB1):c.1877delC(p.Pro626HisfsTer81) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SATB1
NM_002971.6 frameshift
NM_002971.6 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.35
Publications
1 publications found
Genes affected
SATB1 (HGNC:10541): (SATB homeobox 1) This gene encodes a matrix protein which binds nuclear matrix and scaffold-associating DNAs through a unique nuclear architecture. The protein recruits chromatin-remodeling factors in order to regulate chromatin structure and gene expression. [provided by RefSeq, Apr 2016]
TBC1D5 (HGNC:19166): (TBC1 domain family member 5) Enables AP-2 adaptor complex binding activity and retromer complex binding activity. Involved in several processes, including macroautophagy; positive regulation of receptor internalization; and retrograde transport, endosome to Golgi. Located in Golgi apparatus; autophagosome; and endosome membrane. Part of retromer complex. Colocalizes with AP-2 adaptor complex and Atg1/ULK1 kinase complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_pathogenic. The variant received 8 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 6 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 3-18349584-TG-T is Pathogenic according to our data. Variant chr3-18349584-TG-T is described in ClinVar as Pathogenic. ClinVar VariationId is 1335825.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_002971.6. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SATB1 | MANE Select | c.1877delC | p.Pro626HisfsTer81 | frameshift | Exon 11 of 11 | NP_002962.1 | Q01826-1 | ||
| SATB1 | c.1973delC | p.Pro658HisfsTer81 | frameshift | Exon 12 of 12 | NP_001182399.1 | Q01826-2 | |||
| SATB1 | c.1973delC | p.Pro658HisfsTer81 | frameshift | Exon 12 of 12 | NP_001309800.1 | Q01826-2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SATB1 | TSL:1 MANE Select | c.1877delC | p.Pro626HisfsTer81 | frameshift | Exon 11 of 11 | ENSP00000341024.5 | Q01826-1 | ||
| SATB1 | TSL:1 | c.1973delC | p.Pro658HisfsTer81 | frameshift | Exon 12 of 12 | ENSP00000399518.1 | Q01826-2 | ||
| SATB1 | TSL:1 | c.1877delC | p.Pro626HisfsTer81 | frameshift | Exon 11 of 11 | ENSP00000399708.2 | Q01826-1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1461464Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727008
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1461464
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
727008
African (AFR)
AF:
AC:
0
AN:
33468
American (AMR)
AF:
AC:
0
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
0
AN:
86238
European-Finnish (FIN)
AF:
AC:
0
AN:
53400
Middle Eastern (MID)
AF:
AC:
0
AN:
5506
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1111938
Other (OTH)
AF:
AC:
0
AN:
60354
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Pathogenic
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
1
-
-
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
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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