chr11-95813536-C-T

Variant names:

Variant summary

Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PVS1PP5_Moderate

The NM_014679.5(CEP57):c.451C>T(p.Arg151*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,612,864 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. R151R) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)

Exomes 𝑓: 0.000040 ( 0 hom. )

Consequence

CEP57
NM_014679.5 stop_gained

Scores

Clinical Significance

Pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 3.34

Publications

5 publications found

Variant links:

Genes affected

CEP57 (HGNC:30794): (centrosomal protein 57) This gene encodes a cytoplasmic protein called Translokin. This protein localizes to the centrosome and has a function in microtubular stabilization. The N-terminal half of this protein is required for its centrosome localization and for its multimerization, and the C-terminal half is required for nucleating, bundling and anchoring microtubules to the centrosomes. This protein specifically interacts with fibroblast growth factor 2 (FGF2), sorting nexin 6, Ran-binding protein M and the kinesins KIF3A and KIF3B, and thus mediates the nuclear translocation and mitogenic activity of the FGF2. It also interacts with cyclin D1 and controls nucleocytoplasmic distribution of the cyclin D1 in quiescent cells. This protein is crucial for maintaining correct chromosomal number during cell division. Mutations in this gene cause mosaic variegated aneuploidy syndrome, a rare autosomal recessive disorder. Multiple alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Aug 2011]

CEP57 Gene-Disease associations (from GenCC):

mosaic variegated aneuploidy syndrome 2
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
mosaic variegated aneuploidy syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

CEP57 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Pathogenic. The variant received 10 ACMG points.

PVS1

Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.

PP5

Variant 11-95813536-C-T is Pathogenic according to our data. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95813536-C-T is described in CliVar as Pathogenic. Clinvar id is 643769.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP57	NM_014679.5 link	c.451C>T	p.Arg151*	stop_gained	Exon 4 of 11	ENST00000325542.10	NP_055494.2	Q86XR8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP57	ENST00000325542.10 link	c.451C>T	p.Arg151*	stop_gained	Exon 4 of 11	1	NM_014679.5	ENSP00000317902.5		Q86XR8-1

Frequencies

GnomAD3 genomes

AF:

0.00000657

AC:

AN:

152100

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

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:

0.0000147

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00000799

AC:

AN:

250308

AF XY:

0.0000148

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000176

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000404

AC:

AN:

1460764

Hom.:

Cov.:

AF XY:

0.0000344

AC XY:

AN XY:

726730

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33470

American (AMR)

AF:

0.00

AC:

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26126

East Asian (EAS)

AF:

0.00

AC:

AN:

39640

South Asian (SAS)

AF:

0.00

AC:

AN:

86242

European-Finnish (FIN)

AF:

0.00

AC:

AN:

52602

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5726

European-Non Finnish (NFE)

AF:

0.0000513

AC:

AN:

1111864

Other (OTH)

AF:

0.0000331

AC:

AN:

60372

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00000657

AC:

AN:

152100

Hom.:

Cov.:

AF XY:

0.0000135

AC XY:

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41392

American (AMR)

AF:

0.00

AC:

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5202

South Asian (SAS)

AF:

0.00

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10588

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.0000147

AC:

AN:

68022

Other (OTH)

AF:

0.00

AC:

AN:

2088

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000378

EpiCase

AF:

0.00

EpiControl

AF:

0.0000593

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Mosaic variegated aneuploidy syndrome 2

Pathogenic:1

Dec 10, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 643769). This variant has not been reported in the literature in individuals affected with CEP57-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.002%). This sequence change creates a premature translational stop signal (p.Arg151*) in the CEP57 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CEP57 are known to be pathogenic (PMID: 21552266, 24259107). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.61

BayesDel_noAF

Pathogenic

0.60

CADD

Pathogenic

(source)

DANN

Uncertain

1.0

Eigen

Pathogenic

0.89

Eigen_PC

Pathogenic

0.72

FATHMM_MKL

Uncertain

0.79

PhyloP100

3.3

Vest4

0.48

GERP RS

3.9

Mutation Taster

=0/200

disease causing (ClinVar)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over