9-78236351-A-T

Position:

• chr9-78236351-A-T

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1 PM2

The NM_001330691.3(CEP78):​c.1A>T​(p.Met1?) variant causes a start lost change. The variant allele was found at a frequency of 0.000000705 in 1,418,920 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 Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.0e-7 (0 hom.)
• Consequence: CEP78 NM_001330691.3 start_lost
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 5.36

Genes affected

CEP78 (HGNC:25740): (centrosomal protein 78) This gene encodes a centrosomal protein that is both required for the regulation of centrosome-related events during the cell cycle, and required for ciliogenesis. The encoded protein has an N-terminal leucine-rich repeat (LRR) domain with six consecutive LRR repeats, and a C-terminal coiled-coil domain. It interacts with the N-terminal catalytic domain of polo-like kinase 4 (PLK4) and colocalizes with PLK4 to the distal end of the centriole. Naturally occurring mutations in this gene cause defects in primary cilia that result in retinal degeneration and sensorineural hearing loss which are associated with cone-rod degeneration disease as well as Usher syndrome. Low expression of this gene is associated with poor prognosis of colorectal cancer patients. [provided by RefSeq, Mar 2017]

ACMG classification

Verdict is Pathogenic. Variant got 10 ACMG points.

• PVS1: Start lost variant, no new inframe start found.
• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP78	NM_001330691.3	c.1A>T	p.Met1?	start_lost	1/17	ENST00000643273.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP78	ENST00000643273.2	c.1A>T	p.Met1?	start_lost	1/17		NM_001330691.3	P4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.05e-7 AC: 1 AN: 1418920 Hom.: 0 Cov.: 30 AF XY: 0.00000142 AC XY: 1 AN XY: 703194

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: 9.13e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Aug 30, 2023

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 2018416). This variant has not been reported in the literature in individuals affected with CEP78-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change affects the initiator methionine of the CEP78 mRNA. The next in-frame methionine is located at codon 88. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Uncertain	0.12	D
BayesDel_noAF	Uncertain	-0.070
CADD	Pathogenic	26
DANN	Benign	0.94
DEOGEN2	Benign	0.14	T;.;.;.;.;.;.;.;.;T;.;.;.;.
Eigen	Uncertain	0.37
Eigen_PC	Uncertain	0.33
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.90	D;D;D;D;D;D;D;.;D;D;D;D;D;D
M_CAP	Uncertain	0.24	D
MetaRNN	Pathogenic	0.97	D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Benign	-0.66	T
MutationTaster	Benign	1.0	D;D;D;D
PROVEAN	Benign	-1.2	N;.;.;.;.;.;.;N;N;N;.;.;.;N
REVEL	Uncertain	0.32
Sift	Pathogenic	0.0	D;.;.;.;.;.;.;D;D;D;.;.;.;D
Sift4G	Pathogenic	0.0	D;.;.;.;.;.;.;D;D;D;.;.;.;D
Polyphen		0.99	D;.;.;.;.;.;.;.;P;.;.;.;.;.
Vest4		0.72
MutPred		0.99		Loss of ubiquitination at K6 (P = 0.1083);Loss of ubiquitination at K6 (P = 0.1083);Loss of ubiquitination at K6 (P = 0.1083);Loss of ubiquitination at K6 (P = 0.1083);Loss of ubiquitination at K6 (P = 0.1083);Loss of ubiquitination at K6 (P = 0.1083);Loss of ubiquitination at K6 (P = 0.1083);Loss of ubiquitination at K6 (P = 0.1083);Loss of ubiquitination at K6 (P = 0.1083);Loss of ubiquitination at K6 (P = 0.1083);Loss of ubiquitination at K6 (P = 0.1083);Loss of ubiquitination at K6 (P = 0.1083);Loss of ubiquitination at K6 (P = 0.1083);Loss of ubiquitination at K6 (P = 0.1083);
MVP		0.61
ClinPred		1.0	D
GERP RS		4.7
Varity_R		0.96
gMVP		0.55

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

Other links and lift over

dbSNP: rs761538280; hg19: chr9-80851267;