Variant 5-75374136-CTTTT-CT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting

The NM_001379004.1(CERT1):c.1722_1724delAAA(p.Lys575del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 138,498 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: 𝑓 0.000022 ( 0 hom., cov: 31)

Consequence

CERT1
NM_001379004.1 disruptive_inframe_deletion

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]

CERT1 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PM4

Nonframeshift variant in NON repetitive region in NM_001379004.1. Strenght limited to Supporting due to length of the change: 1aa.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	Protein	UniProt
CERT1	NM_001379004.1 link	c.1722_1724delAAA	p.Lys575del	disruptive_inframe_deletion	Exon 16 of 16	NP_001365933.1
CERT1	XM_011543090.4 link	c.1800_1802delAAA	p.Lys601del	disruptive_inframe_deletion	Exon 17 of 17	XP_011541392.1
CERT1	NM_001130105.1 link	c.62_64delAAA		3_prime_UTR_variant	Exon 19 of 19	NP_001123577.1	Q9Y5P4-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	Protein	UniProt
CERT1	ENST00000261415.12 link	c.9+5198_9+5200delAAA		intron_variant	Intron 17 of 17	1	ENSP00000261415.8	Q9Y5P4-1
CERT1	ENST00000642556.1 link	c.1722_1724delAAA	p.Lys575del	disruptive_inframe_deletion	Exon 16 of 16		ENSP00000496016.1	A0A2R8Y7C5
CERT1	ENST00000644072 link	c.62_64delAAA		3_prime_UTR_variant	Exon 18 of 18		ENSP00000494110.2	Q9Y5P4-1

Frequencies

GnomAD3 genomes

AF:

0.0000217

AC:

AN:

138498

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000803

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

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:

0.00

Gnomad OTH

AF:

0.00

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0000217

AC:

AN:

138498

Hom.:

Cov.:

AF XY:

0.0000300

AC XY:

AN XY:

66616

show subpopulations

Gnomad4 AFR

AF:

0.0000803

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over