rs1135402915
Variant names:
Variant summary
Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001300902.2(CD55):c.110delG(p.Gly37AlafsTer24) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,642 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
CD55
NM_001300902.2 frameshift
NM_001300902.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.524
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: Labcorp Genetics (formerly Invitae), Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 11 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 1-207322389-TG-T is Pathogenic according to our data. Variant chr1-207322389-TG-T is described in ClinVar as Pathogenic. ClinVar VariationId is 431760.Status of the report is no_assertion_criteria_provided, 0 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001300902.2. 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 |
|---|---|---|---|---|---|---|---|---|---|
| CD55 | NM_000574.5 | MANE Select | c.110delG | p.Gly37AlafsTer24 | frameshift | Exon 2 of 10 | NP_000565.1 | ||
| CD55 | NM_001300902.2 | c.110delG | p.Gly37AlafsTer24 | frameshift | Exon 2 of 10 | NP_001287831.1 | |||
| CD55 | NM_001114752.3 | c.110delG | p.Gly37AlafsTer24 | frameshift | Exon 2 of 11 | NP_001108224.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CD55 | ENST00000367064.9 | TSL:1 MANE Select | c.110delG | p.Gly37AlafsTer24 | frameshift | Exon 2 of 10 | ENSP00000356031.4 | ||
| CD55 | ENST00000367063.6 | TSL:1 | c.110delG | p.Gly37AlafsTer24 | frameshift | Exon 2 of 10 | ENSP00000356030.2 | ||
| CD55 | ENST00000314754.12 | TSL:1 | c.110delG | p.Gly37AlafsTer24 | frameshift | Exon 2 of 11 | ENSP00000316333.8 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461642Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727126 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1461642
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
727126
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33478
American (AMR)
AF:
AC:
0
AN:
44718
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26130
East Asian (EAS)
AF:
AC:
0
AN:
39698
South Asian (SAS)
AF:
AC:
0
AN:
86246
European-Finnish (FIN)
AF:
AC:
0
AN:
53420
Middle Eastern (MID)
AF:
AC:
0
AN:
5766
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1111800
Other (OTH)
AF:
AC:
1
AN:
60386
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
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.:
33
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Pathogenic
Revision:no assertion criteria provided
Pathogenic
VUS
Benign
Condition
1
-
-
Protein-losing enteropathy (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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