17-46938605-CAGA-C
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2PM4_SupportingPP5
The NM_004287.5(GOSR2):c.491_493delAGA(p.Lys164del) variant causes a disruptive inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,570 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
GOSR2
NM_004287.5 disruptive_inframe_deletion
NM_004287.5 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.85
Publications
7 publications found
Genes affected
GOSR2 (HGNC:4431): (golgi SNAP receptor complex member 2) This gene encodes a trafficking membrane protein which transports proteins among the medial- and trans-Golgi compartments. Due to its chromosomal location and trafficking function, this gene may be involved in familial essential hypertension. [provided by RefSeq, Mar 2016]
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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;
PM4
Nonframeshift variant in NON repetitive region in NM_004287.5. Strenght limited to Supporting due to length of the change: 1aa.
PP5
Variant 17-46938605-CAGA-C is Pathogenic according to our data. Variant chr17-46938605-CAGA-C is described in ClinVar as Pathogenic. ClinVar VariationId is 208982.Status of the report is no_assertion_criteria_provided, 0 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_004287.5. 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 |
|---|---|---|---|---|---|---|---|---|---|
| GOSR2 | NM_004287.5 | MANE Select | c.491_493delAGA | p.Lys164del | disruptive_inframe_deletion | Exon 6 of 6 | NP_004278.2 | ||
| GOSR2 | NM_001321133.2 | c.491_493delAGA | p.Lys164del | disruptive_inframe_deletion | Exon 6 of 7 | NP_001308062.1 | |||
| GOSR2 | NM_054022.4 | c.491_493delAGA | p.Lys164del | disruptive_inframe_deletion | Exon 6 of 7 | NP_473363.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| GOSR2 | ENST00000640051.2 | TSL:1 MANE Select | c.491_493delAGA | p.Lys164del | disruptive_inframe_deletion | Exon 6 of 6 | ENSP00000492751.1 | ||
| GOSR2 | ENST00000225567.9 | TSL:1 | c.491_493delAGA | p.Lys164del | disruptive_inframe_deletion | Exon 6 of 7 | ENSP00000225567.4 | ||
| ENSG00000262633 | ENST00000571841.1 | TSL:5 | n.491_493delAGA | non_coding_transcript_exon | Exon 6 of 10 | ENSP00000461460.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461570Hom.: 0 AF XY: 0.00000138 AC XY: 1AN XY: 727118 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1461570
Hom.:
AF XY:
AC XY:
1
AN XY:
727118
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33466
American (AMR)
AF:
AC:
0
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39696
South Asian (SAS)
AF:
AC:
0
AN:
86254
European-Finnish (FIN)
AF:
AC:
0
AN:
53416
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1111726
Other (OTH)
AF:
AC:
0
AN:
60384
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Progressive myoclonic epilepsy type 6 Pathogenic:1
Mar 22, 2021
OMIM
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:literature only
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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