17-81868810-TG-TGGGGGGG
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM4
The NM_001301242.2(ARHGDIA):c.563_568dupCCCCCC(p.Pro188_Pro189dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ARHGDIA
NM_001301242.2 conservative_inframe_insertion
NM_001301242.2 conservative_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0640
Publications
0 publications found
Genes affected
ARHGDIA (HGNC:678): (Rho GDP dissociation inhibitor alpha) This gene encodes a protein that plays a key role in the regulation of signaling through Rho GTPases. The encoded protein inhibits the disassociation of Rho family members from GDP (guanine diphosphate), thereby maintaining these factors in an inactive state. Activity of this protein is important in a variety of cellular processes, and expression of this gene may be altered in tumors. Mutations in this gene have been found in individuals with nephrotic syndrome, type 8. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
ARHGDIA Gene-Disease associations (from GenCC):
- nephrotic syndrome, type 8Inheritance: AR Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen
- familial idiopathic steroid-resistant nephrotic syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_001301242.2.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001301242.2. 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 |
|---|---|---|---|---|---|---|---|---|---|
| ARHGDIA | MANE Select | c.*60_*65dupCCCCCC | 3_prime_UTR | Exon 6 of 6 | NP_004300.1 | P52565-1 | |||
| ARHGDIA | c.563_568dupCCCCCC | p.Pro188_Pro189dup | conservative_inframe_insertion | Exon 7 of 7 | NP_001288171.1 | ||||
| ARHGDIA | c.*60_*65dupCCCCCC | 3_prime_UTR | Exon 5 of 5 | NP_001288172.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ARHGDIA | TSL:1 MANE Select | c.*60_*65dupCCCCCC | 3_prime_UTR | Exon 6 of 6 | ENSP00000269321.7 | P52565-1 | |||
| ARHGDIA | TSL:1 | c.*60_*65dupCCCCCC | 3_prime_UTR | Exon 5 of 5 | ENSP00000464205.1 | P52565-1 | |||
| ARHGDIA | TSL:3 | c.563_568dupCCCCCC | p.Pro188_Pro189dup | conservative_inframe_insertion | Exon 7 of 7 | ENSP00000462209.1 | J3KRY1 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 40932Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
0
AN:
40932
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
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Gnomad ASJ
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Gnomad EAS
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Gnomad FIN
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Gnomad NFE
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Gnomad OTH
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 396948Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 216816
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
396948
Hom.:
Cov.:
35
AF XY:
AC XY:
0
AN XY:
216816
African (AFR)
AF:
AC:
0
AN:
11504
American (AMR)
AF:
AC:
0
AN:
29104
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
10586
East Asian (EAS)
AF:
AC:
0
AN:
11658
South Asian (SAS)
AF:
AC:
0
AN:
49562
European-Finnish (FIN)
AF:
AC:
0
AN:
24972
Middle Eastern (MID)
AF:
AC:
0
AN:
2704
European-Non Finnish (NFE)
AF:
AC:
0
AN:
240296
Other (OTH)
AF:
AC:
0
AN:
16562
GnomAD4 genome 0.00 AC: 0AN: 40932Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 20206
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
40932
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
20206
African (AFR)
AF:
AC:
0
AN:
10526
American (AMR)
AF:
AC:
0
AN:
3798
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
990
East Asian (EAS)
AF:
AC:
0
AN:
2018
South Asian (SAS)
AF:
AC:
0
AN:
1352
European-Finnish (FIN)
AF:
AC:
0
AN:
2084
Middle Eastern (MID)
AF:
AC:
0
AN:
164
European-Non Finnish (NFE)
AF:
AC:
0
AN:
19222
Other (OTH)
AF:
AC:
0
AN:
540
ClinVar
Not reported inComputational 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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