8-21999163-T-G

Position:

• chr8-21999163-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP2

The NM_015024.5(XPO7):​c.2501T>G​(p.Ile834Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: XPO7 NM_015024.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 8.02

Genes affected

XPO7 (HGNC:14108): (exportin 7) The transport of protein and large RNAs through the nuclear pore complexes (NPC) is an energy-dependent and regulated process. The import of proteins with a nuclear localization signal (NLS) is accomplished by recognition of one or more clusters of basic amino acids by the importin-alpha/beta complex; see MIM 600685 and MIM 602738. The small GTPase RAN (MIM 601179) plays a key role in NLS-dependent protein import. RAN-binding protein-16 is a member of the importin-beta superfamily of nuclear transport receptors.[supplied by OMIM, Jul 2002]

XPO7 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), XPO7. . Gene score misZ 4.8157 (greater than the threshold 3.09). Trascript score misZ 5.4671 (greater than threshold 3.09). GenCC has associacion of gene with prostate cancer.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
XPO7	NM_015024.5	c.2501T>G	p.Ile834Ser	missense_variant	23/28	ENST00000252512.14	NP_055839.3
XPO7	NM_001100161.2	c.2528T>G	p.Ile843Ser	missense_variant	23/28		NP_001093631.1
XPO7	NM_001362802.2	c.2435T>G	p.Ile812Ser	missense_variant	22/27		NP_001349731.1
XPO7	NR_156173.2	n.2721T>G		non_coding_transcript_exon_variant	24/29

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
XPO7	ENST00000252512.14	c.2501T>G	p.Ile834Ser	missense_variant	23/28	1	NM_015024.5	ENSP00000252512.9
XPO7	ENST00000433566.8	c.2504T>G	p.Ile835Ser	missense_variant	23/28	5		ENSP00000410249.3
XPO7	ENST00000517551.2	c.431T>G	p.Ile144Ser	missense_variant	5/6	5		ENSP00000429317.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

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

Sep 08, 2024

The c.2501T>G (p.I834S) alteration is located in exon 23 (coding exon 23) of the XPO7 gene. This alteration results from a T to G substitution at nucleotide position 2501, causing the isoleucine (I) at amino acid position 834 to be replaced by a serine (S). 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	Pathogenic	0.73
BayesDel_addAF	Uncertain	0.14	D
BayesDel_noAF	Uncertain	-0.040
CADD	Uncertain	26
DANN	Uncertain	0.99
DEOGEN2	Benign	0.29	T;.;T
Eigen	Uncertain	0.22
Eigen_PC	Uncertain	0.39
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Uncertain	0.96	D;D;D
M_CAP	Benign	0.012	T
MetaRNN	Uncertain	0.56	D;D;D
MetaSVM	Benign	-0.93	T
MutationAssessor	Benign	1.7	L;.;.
PrimateAI	Uncertain	0.73	T
PROVEAN	Pathogenic	-4.4	D;D;.
REVEL	Uncertain	0.31
Sift	Benign	0.046	D;D;.
Sift4G	Benign	0.079	T;T;D
Polyphen		0.0040	B;B;.
Vest4		0.88
MVP		0.19
MPC		0.76
ClinPred		0.97	D
GERP RS		5.9
Varity_R		0.55
gMVP		0.82

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: chr8-21856674;