5-90405724-C-G

Position:

• chr5-90405724-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_004365.4(CETN3):​c.229G>C​(p.Ala77Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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: 31)
• Consequence: CETN3 NM_004365.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.22

Genes affected

CETN3 (HGNC:1868): (centrin 3) The protein encoded by this gene contains four EF-hand calcium binding domains, and is a member of the centrin protein family. Centrins are evolutionarily conserved proteins similar to the CDC31 protein of S. cerevisiae. Yeast CDC31 is located at the centrosome of interphase and mitotic cells, where it plays a fundamental role in centrosome duplication and separation. Multiple forms of the proteins similar to the yeast centrin have been identified in human and other mammalian cells, some of which have been shown to be associated with centrosome fractions. This protein appears to be one of the most abundant centrins associated with centrosome, which suggests a similar function to its yeast counterpart. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.21250969).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CETN3	NM_004365.4	c.229G>C	p.Ala77Pro	missense_variant	3/5	ENST00000283122.8
CETN3	NM_001297765.2	c.229G>C	p.Ala77Pro	missense_variant	3/6
CETN3	NM_001297768.2	c.229G>C	p.Ala77Pro	missense_variant	3/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CETN3	ENST00000283122.8	c.229G>C	p.Ala77Pro	missense_variant	3/5	1	NM_004365.4	P1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 31

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 16, 2023

The c.229G>C (p.A77P) alteration is located in exon 3 (coding exon 3) of the CETN3 gene. This alteration results from a G to C substitution at nucleotide position 229, causing the alanine (A) at amino acid position 77 to be replaced by a proline (P). 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	Uncertain	0.54
BayesDel_addAF	Uncertain	0.023	T
BayesDel_noAF	Benign	-0.20
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.052	T;.;.;.;T
Eigen	Benign	-0.12
Eigen_PC	Benign	0.078
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Uncertain	0.91	D;D;D;D;D
M_CAP	Benign	0.052	D
MetaRNN	Benign	0.21	T;T;T;T;T
MetaSVM	Benign	-0.72	T
MutationAssessor	Benign	0.55	N;.;.;.;.
MutationTaster	Benign	0.91	D;D;D;D;D
PrimateAI	Uncertain	0.63	T
PROVEAN	Benign	-1.2	N;N;N;N;N
REVEL	Benign	0.24
Sift	Uncertain	0.0030	D;D;D;D;D
Sift4G	Uncertain	0.052	T;D;D;T;T
Polyphen		0.029	B;.;.;.;.
Vest4		0.24
MutPred		0.44		Gain of methylation at K80 (P = 0.0461);Gain of methylation at K80 (P = 0.0461);Gain of methylation at K80 (P = 0.0461);Gain of methylation at K80 (P = 0.0461);Gain of methylation at K80 (P = 0.0461);
MVP		0.76
MPC		0.25
ClinPred		0.80	D
GERP RS		4.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.42
gMVP		0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: chr5-89701541;