rs1363632175
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely pathogenic. The variant received 6 ACMG points: 6P and 0B. PVS1_StrongPM2
The ENST00000592860.3(CFD):c.54C>A(p.Cys18*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CFD
ENST00000592860.3 stop_gained
ENST00000592860.3 stop_gained
Scores
1
2
4
Splicing: ADA: 0.000008225
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.24
Publications
0 publications found
Genes affected
CFD (HGNC:2771): (complement factor D) This gene encodes a member of the S1, or chymotrypsin, family of serine peptidases. This protease catalyzes the cleavage of factor B, the rate-limiting step of the alternative pathway of complement activation. This protein also functions as an adipokine, a cell signaling protein secreted by adipocytes, which regulates insulin secretion in mice. Mutations in this gene underlie complement factor D deficiency, which is associated with recurrent bacterial meningitis infections in human patients. Alternative splicing of this gene results in multiple transcript variants. At least one of these variants encodes a preproprotein that is proteolytically processed to generate the mature protease. [provided by RefSeq, Nov 2015]
CFD Gene-Disease associations (from GenCC):
- recurrent Neisseria infections due to factor D deficiencyInheritance: AR Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
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ACMG classification
Classification was made for transcript
Our verdict: Likely_pathogenic. The variant received 6 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 7 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1416750Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 700786
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1416750
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
700786
African (AFR)
AF:
AC:
0
AN:
32650
American (AMR)
AF:
AC:
0
AN:
38060
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25354
East Asian (EAS)
AF:
AC:
0
AN:
37674
South Asian (SAS)
AF:
AC:
0
AN:
80742
European-Finnish (FIN)
AF:
AC:
0
AN:
49358
Middle Eastern (MID)
AF:
AC:
0
AN:
5560
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1088746
Other (OTH)
AF:
AC:
0
AN:
58606
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
PhyloP100
Vest4
GERP RS
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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