rs1294237377

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PP3

The NM_201253.3(CRB1):​c.2380C>A​(p.His794Asn) variant causes a missense 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. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

CRB1
NM_201253.3 missense

Scores

3
7
9

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.69
Variant links:
Genes affected
CRB1 (HGNC:2343): (crumbs cell polarity complex component 1) This gene encodes a protein which is similar to the Drosophila crumbs protein and localizes to the inner segment of mammalian photoreceptors. In Drosophila crumbs localizes to the stalk of the fly photoreceptor and may be a component of the molecular scaffold that controls proper development of polarity in the eye. Mutations in this gene are associated with a severe form of retinitis pigmentosa, RP12, and with Leber congenital amaurosis. Alternate splicing results in multiple transcript variants, some protein coding and some non-protein coding.[provided by RefSeq, Apr 2012]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 5 ACMG points.

PM1
In a domain Laminin G-like 2 (size 171) in uniprot entity CRUM1_HUMAN there are 53 pathogenic changes around while only 2 benign (96%) in NM_201253.3
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.795

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CRB1NM_201253.3 linkuse as main transcriptc.2380C>A p.His794Asn missense_variant 7/12 ENST00000367400.8 NP_957705.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CRB1ENST00000367400.8 linkuse as main transcriptc.2380C>A p.His794Asn missense_variant 7/121 NM_201253.3 ENSP00000356370 P1P82279-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32

ClinVar

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

Submissions by phenotype

Retinitis pigmentosa 12;C3151202:Leber congenital amaurosis 8 Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJun 12, 2017In summary, this variant has uncertain impact on CRB1 function. The available evidence is currently insufficient to determine its role in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C25"). This variant has not been reported in the literature in individuals with a CRB1-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces histidine with asparagine at codon 794 of the CRB1 protein (p.His794Asn). The histidine residue is highly conserved and there is a small physicochemical difference between histidine and asparagine. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.17
BayesDel_addAF
Uncertain
0.065
T
BayesDel_noAF
Benign
-0.14
CADD
Benign
20
DANN
Uncertain
0.98
DEOGEN2
Uncertain
0.63
D;.;D;.;T
Eigen
Uncertain
0.24
Eigen_PC
Benign
0.18
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Benign
0.71
T;.;T;T;T
M_CAP
Pathogenic
0.42
D
MetaRNN
Pathogenic
0.79
D;D;D;D;D
MetaSVM
Uncertain
0.49
D
MutationAssessor
Benign
1.9
.;L;L;.;.
MutationTaster
Benign
1.0
D;D;D;D;D;D;D
PrimateAI
Benign
0.46
T
PROVEAN
Uncertain
-4.3
D;.;D;D;D
REVEL
Uncertain
0.63
Sift
Benign
0.079
T;.;T;D;D
Sift4G
Benign
0.14
T;.;T;D;D
Polyphen
0.80
P;.;B;D;.
Vest4
0.35
MutPred
0.69
.;Loss of ubiquitination at K799 (P = 0.1216);Loss of ubiquitination at K799 (P = 0.1216);.;.;
MVP
0.94
MPC
0.036
ClinPred
0.70
D
GERP RS
5.5
Varity_R
0.23
gMVP
0.92

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs1294237377; hg19: chr1-197396835; API