6-53095591-C-A

Variant names:

• chr6-53095591-C-A
• NM_033480.3:c.1132C>A

Variant summary

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

The NM_033480.3(FBXO9):​c.1132C>A​(p.Gln378Lys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: FBXO9 NM_033480.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.57

Genes affected

FBXO9 (HGNC:13588): (F-box protein 9) This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of the ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbxs class. Alternative splicing of this gene generates at least 3 transcript variants diverging at the 5' terminus. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FBXO9	NM_033480.3	c.1132C>A	p.Gln378Lys	missense_variant	Exon 12 of 13	ENST00000323557.12	NP_258441.1
FBXO9	NM_012347.4	c.1162C>A	p.Gln388Lys	missense_variant	Exon 11 of 12		NP_036479.1
FBXO9	NM_033481.3	c.1030C>A	p.Gln344Lys	missense_variant	Exon 12 of 13		NP_258442.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FBXO9	ENST00000323557.12	c.1132C>A	p.Gln378Lys	missense_variant	Exon 12 of 13	1	NM_033480.3	ENSP00000326968.7
FBXO9	ENST00000244426.10	c.1162C>A	p.Gln388Lys	missense_variant	Exon 11 of 12	1		ENSP00000244426.6
FBXO9	ENST00000370939.7	c.1030C>A	p.Gln344Lys	missense_variant	Exon 12 of 13	1		ENSP00000359977.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Mar 08, 2025

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1162C>A (p.Q388K) alteration is located in exon 11 (coding exon 11) of the FBXO9 gene. This alteration results from a C to A substitution at nucleotide position 1162, causing the glutamine (Q) at amino acid position 388 to be replaced by a lysine (K). 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	Benign	0.22
BayesDel_addAF	Uncertain	0.027	T
BayesDel_noAF	Benign	-0.20
CADD	Benign	22
DANN	Uncertain	0.98
DEOGEN2	Benign	0.075	.;.;T;.
Eigen	Uncertain	0.36
Eigen_PC	Uncertain	0.43
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.93	D;D;D;D
M_CAP	Benign	0.023	T
MetaRNN	Uncertain	0.46	T;T;T;T
MetaSVM	Benign	-0.74	T
MutationAssessor	Benign	1.7	.;.;L;.
PrimateAI	Uncertain	0.70	T
PROVEAN	Benign	-1.4	N;N;N;.
REVEL	Benign	0.21
Sift	Benign	0.051	T;D;T;.
Sift4G	Benign	0.22	T;T;T;T
Polyphen		0.52, 0.060	.;P;B;.
Vest4		0.29
MutPred		0.48		.;.;Loss of sheet (P = 0.0037);.;
MVP		0.64
MPC		0.59
ClinPred		0.72	D
GERP RS		5.1
Varity_R		0.19
gMVP		0.41

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-52960389;