5-75379360-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001379029.1(CERT1):​c.1861C>T​(p.Pro621Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

CERT1
NM_001379029.1 missense

Scores

1
9
9

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.79
Variant links:
Genes affected
CERT1 (HGNC:2205): (ceramide transporter 1) This gene encodes a kinase that specifically phosphorylates the N-terminal region of the non-collagenous domain of the alpha 3 chain of type IV collagen, known as the Goodpasture antigen. Goodpasture disease is the result of an autoimmune response directed at this antigen. One isoform of this protein is also involved in ceramide intracellular transport. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.36465168).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CERT1NM_001379029.1 linkc.1861C>T p.Pro621Ser missense_variant Exon 17 of 17 ENST00000643780.2 NP_001365958.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CERT1ENST00000643780.2 linkc.1861C>T p.Pro621Ser missense_variant Exon 17 of 17 NM_001379029.1 ENSP00000495760.1 Q9Y5P4-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

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

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Aug 24, 2020
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The alteration results in an amino acid change:_x000D_ _x000D_ The c.2245C>T (p.P749S) alteration is located in coding exon 18 of the CERT1 gene. This alteration results from a C to T substitution at nucleotide position 2245, causing the proline (P) at amino acid position 749 to be replaced by a serine (S). The alteration is not observed in population databases:_x000D_ _x000D_ Based on data from the Genome Aggregation Database (gnomAD), the COL4A3BP c.2245C>T alteration was not observed, with coverage at this position. The altered amino acid is conserved throughout evolution:_x000D_ _x000D_ The p.P749 amino acid is conserved in available vertebrate species; however, serine (S) is the reference amino acid in a few species. The alteration is predicted tolerated by in silico modeling:_x000D_ _x000D_ The p.P749S alteration is predicted to be tolerated by in silico analysis. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.081
BayesDel_addAF
Benign
-0.043
T
BayesDel_noAF
Benign
-0.30
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.66
.;.;D;.;.;.;.;D;D;.;.
Eigen
Uncertain
0.19
Eigen_PC
Uncertain
0.35
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Uncertain
0.93
.;D;.;.;D;D;.;.;D;D;D
M_CAP
Benign
0.011
T
MetaRNN
Benign
0.36
T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.7
.;.;L;.;.;.;.;L;L;.;.
PrimateAI
Uncertain
0.74
T
PROVEAN
Pathogenic
-5.5
.;.;.;.;.;.;.;D;.;.;.
REVEL
Benign
0.13
Sift
Uncertain
0.019
.;.;.;.;.;.;.;D;.;.;.
Sift4G
Uncertain
0.013
.;.;.;.;.;.;.;D;.;.;.
Polyphen
0.0040
B;B;B;.;.;.;B;B;B;.;B
Vest4
0.23
MutPred
0.49
.;.;Gain of MoRF binding (P = 0.038);.;.;.;.;Gain of MoRF binding (P = 0.038);Gain of MoRF binding (P = 0.038);.;.;
MVP
0.32
ClinPred
0.98
D
GERP RS
5.8
Varity_R
0.60
gMVP
0.76

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.060
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-74675185; API