rs545323650

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2

The NM_001379004.1(CERT1):​c.1721_1724delAAAA​(p.Lys574SerfsTer2) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000482 in 207,516 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000048 ( 0 hom. )

Consequence

CERT1
NM_001379004.1 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.33
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 4 ACMG points.

PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.0534 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CERT1NM_001379004.1 linkc.1721_1724delAAAA p.Lys574SerfsTer2 frameshift_variant Exon 16 of 16 NP_001365933.1
CERT1XM_011543090.4 linkc.1799_1802delAAAA p.Lys600SerfsTer2 frameshift_variant Exon 17 of 17 XP_011541392.1
CERT1NM_001130105.1 linkc.*61_*64delAAAA 3_prime_UTR_variant Exon 19 of 19 NP_001123577.1 Q9Y5P4-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CERT1ENST00000261415.12 linkc.*9+5197_*9+5200delAAAA intron_variant Intron 17 of 17 1 ENSP00000261415.8 Q9Y5P4-1
CERT1ENST00000642556.1 linkc.1721_1724delAAAA p.Lys574SerfsTer2 frameshift_variant Exon 16 of 16 ENSP00000496016.1 A0A2R8Y7C5
CERT1ENST00000644072 linkc.*61_*64delAAAA 3_prime_UTR_variant Exon 18 of 18 ENSP00000494110.2 Q9Y5P4-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
0.00000482
AC:
1
AN:
207516
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
105484
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000751
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs545323650; hg19: chr5-74669961; API