rs1654419461
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely pathogenic. The variant received 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_000574.5(CD55):c.98G>A(p.Trp33*) variant causes a stop gained, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000584 in 1,370,064 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000058 ( 0 hom. )
Consequence
CD55
NM_000574.5 stop_gained, splice_region
NM_000574.5 stop_gained, splice_region
Scores
1
5
Splicing: ADA: 0.00002263
2
Clinical Significance
Conservation
PhyloP100: -1.27
Publications
0 publications found
Genes affected
CD55 (HGNC:2665): (CD55 molecule (Cromer blood group)) This gene encodes a glycoprotein involved in the regulation of the complement cascade. Binding of the encoded protein to complement proteins accelerates their decay, thereby disrupting the cascade and preventing damage to host cells. Antigens present on this protein constitute the Cromer blood group system (CROM). Alternative splicing results in multiple transcript variants. The predominant transcript variant encodes a membrane-bound protein, but alternatively spliced transcripts may produce soluble proteins. [provided by RefSeq, Jul 2014]
CD55 Gene-Disease associations (from GenCC):
- protein-losing enteropathyInheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
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 located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 17 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 1-207321863-G-A is Pathogenic according to our data. Variant chr1-207321863-G-A is described in ClinVar as Pathogenic. ClinVar VariationId is 3338382.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000574.5. 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 |
|---|---|---|---|---|---|---|---|---|---|
| CD55 | NM_000574.5 | MANE Select | c.98G>A | p.Trp33* | stop_gained splice_region | Exon 1 of 10 | NP_000565.1 | P08174-1 | |
| CD55 | NM_001300902.2 | c.98G>A | p.Trp33* | stop_gained splice_region | Exon 1 of 10 | NP_001287831.1 | B1AP13 | ||
| CD55 | NM_001114752.3 | c.98G>A | p.Trp33* | stop_gained splice_region | Exon 1 of 11 | NP_001108224.1 | P08174-2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CD55 | ENST00000367064.9 | TSL:1 MANE Select | c.98G>A | p.Trp33* | stop_gained splice_region | Exon 1 of 10 | ENSP00000356031.4 | P08174-1 | |
| CD55 | ENST00000367063.6 | TSL:1 | c.98G>A | p.Trp33* | stop_gained splice_region | Exon 1 of 10 | ENSP00000356030.2 | B1AP13 | |
| CD55 | ENST00000314754.12 | TSL:1 | c.98G>A | p.Trp33* | stop_gained splice_region | Exon 1 of 11 | ENSP00000316333.8 | P08174-2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000584 AC: 8AN: 1370064Hom.: 0 Cov.: 30 AF XY: 0.00000296 AC XY: 2AN XY: 675462 show subpopulations
GnomAD4 exome
AF:
AC:
8
AN:
1370064
Hom.:
Cov.:
30
AF XY:
AC XY:
2
AN XY:
675462
show subpopulations
African (AFR)
AF:
AC:
0
AN:
30414
American (AMR)
AF:
AC:
0
AN:
34306
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24552
East Asian (EAS)
AF:
AC:
0
AN:
34974
South Asian (SAS)
AF:
AC:
0
AN:
78234
European-Finnish (FIN)
AF:
AC:
0
AN:
34918
Middle Eastern (MID)
AF:
AC:
0
AN:
4048
European-Non Finnish (NFE)
AF:
AC:
8
AN:
1071592
Other (OTH)
AF:
AC:
0
AN:
57026
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.494
Heterozygous variant carriers
0
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2
2
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4
0.00
0.20
0.40
0.60
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
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10
<30
30-35
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Age
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
ClinVar submissions
View on ClinVar Significance:Pathogenic
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
1
-
-
Protein-losing enteropathy (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
PhyloP100
Vest4
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
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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