1-207506809-A-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_000651.6(CR1):ā€‹c.397A>Gā€‹(p.Lys133Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000653 in 1,611,756 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.00060 ( 0 hom., cov: 32)
Exomes š‘“: 0.00066 ( 1 hom. )

Consequence

CR1
NM_000651.6 missense

Scores

1
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.810
Variant links:
Genes affected
CR1 (HGNC:2334): (complement C3b/C4b receptor 1 (Knops blood group)) This gene is a member of the receptors of complement activation (RCA) family and is located in the 'cluster RCA' region of chromosome 1. The genome is polymorphic at this locus with allele-specific splice variants encoding different isoforms, based on the presence/absence of long homologous repeats (LHRs). The gene encodes a monomeric single-pass type I membrane glycoprotein found on erythrocytes, leukocytes, glomerular podocytes, and splenic follicular dendritic cells. The Knops blood group system is a system of antigens located on this protein. The protein mediates cellular binding to particles and immune complexes that have activated complement. Decreases in expression of this protein and/or mutations in this gene have been associated with gallbladder carcinomas, mesangiocapillary glomerulonephritis, systemic lupus erythematosus, sarcoidosis and Alzheimer's disease. Mutations in this gene have also been associated with a reduction in Plasmodium falciparum rosetting, conferring protection against severe malaria. [provided by RefSeq, May 2020]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.021124601).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CR1NM_000651.6 linkc.397A>G p.Lys133Glu missense_variant Exon 3 of 47 ENST00000367049.9 NP_000642.3 P17927E9PDY4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CR1ENST00000367049.9 linkc.397A>G p.Lys133Glu missense_variant Exon 3 of 47 5 NM_000651.6 ENSP00000356016.4 E9PDY4

Frequencies

GnomAD3 genomes
AF:
0.000604
AC:
92
AN:
152232
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00144
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000867
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.000286
AC:
71
AN:
248602
Hom.:
0
AF XY:
0.000296
AC XY:
40
AN XY:
134912
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000380
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000479
Gnomad OTH exome
AF:
0.000664
GnomAD4 exome
AF:
0.000658
AC:
960
AN:
1459406
Hom.:
1
Cov.:
29
AF XY:
0.000647
AC XY:
470
AN XY:
726116
show subpopulations
Gnomad4 AFR exome
AF:
0.000120
Gnomad4 AMR exome
AF:
0.000515
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000187
Gnomad4 NFE exome
AF:
0.000797
Gnomad4 OTH exome
AF:
0.000779
GnomAD4 genome
AF:
0.000604
AC:
92
AN:
152350
Hom.:
0
Cov.:
32
AF XY:
0.000604
AC XY:
45
AN XY:
74508
show subpopulations
Gnomad4 AFR
AF:
0.000241
Gnomad4 AMR
AF:
0.00144
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000867
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.000672
Hom.:
0
Bravo
AF:
0.000850
TwinsUK
AF:
0.000539
AC:
2
ALSPAC
AF:
0.00104
AC:
4
ESP6500AA
AF:
0.000266
AC:
1
ESP6500EA
AF:
0.00109
AC:
9
ExAC
AF:
0.000224
AC:
27
EpiCase
AF:
0.000766
EpiControl
AF:
0.000356

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

KNOPS BLOOD GROUP SYSTEM;C1970028:Malaria, susceptibility to Uncertain:1
Feb 26, 2024
Fulgent Genetics, Fulgent Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.089
BayesDel_addAF
Benign
-0.28
T
BayesDel_noAF
Benign
-0.28
CADD
Benign
0.32
DANN
Benign
0.075
Eigen
Benign
-2.3
Eigen_PC
Benign
-2.3
FATHMM_MKL
Benign
0.0011
N
LIST_S2
Benign
0.023
.;.;.;T;T
M_CAP
Benign
0.0032
T
MetaRNN
Benign
0.021
T;T;T;T;T
MetaSVM
Benign
-1.0
T
PrimateAI
Benign
0.25
T
PROVEAN
Benign
0.040
N;N;N;N;N
REVEL
Uncertain
0.33
Sift
Benign
1.0
T;T;T;T;T
Sift4G
Benign
1.0
T;T;T;T;T
Polyphen
0.0050, 0.0
.;.;.;B;B
Vest4
0.059
MVP
0.34
MPC
0.092
ClinPred
0.014
T
GERP RS
-7.7
gMVP
0.30

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs183171969; hg19: chr1-207680154; API