rs200806311

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001011720.2(XKR9):​c.479C>A​(p.Ala160Glu) 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. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A160V) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

XKR9
NM_001011720.2 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.907
Variant links:
Genes affected
XKR9 (HGNC:20937): (XK related 9) Predicted to enable phospholipid scramblase activity. Predicted to be involved in apoptotic process involved in development; engulfment of apoptotic cell; and phosphatidylserine exposure on apoptotic cell surface. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

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=0.25623193).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
XKR9NM_001011720.2 linkc.479C>A p.Ala160Glu missense_variant Exon 4 of 5 ENST00000408926.8 NP_001011720.1 Q5GH70

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
XKR9ENST00000408926.8 linkc.479C>A p.Ala160Glu missense_variant Exon 4 of 5 1 NM_001011720.2 ENSP00000386141.3 Q5GH70

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.17
T
BayesDel_noAF
Benign
-0.49
CADD
Benign
3.7
DANN
Benign
0.87
DEOGEN2
Benign
0.061
T;T
Eigen
Benign
-0.71
Eigen_PC
Benign
-0.91
FATHMM_MKL
Benign
0.031
N
LIST_S2
Benign
0.48
.;T
M_CAP
Benign
0.031
D
MetaRNN
Benign
0.26
T;T
MetaSVM
Benign
-0.90
T
MutationAssessor
Uncertain
2.7
M;M
PrimateAI
Benign
0.26
T
PROVEAN
Uncertain
-2.7
D;D
REVEL
Benign
0.20
Sift
Benign
0.51
T;T
Sift4G
Benign
0.46
T;T
Polyphen
0.83
P;P
Vest4
0.28
MutPred
0.72
Gain of solvent accessibility (P = 0.0068);Gain of solvent accessibility (P = 0.0068);
MVP
0.52
MPC
0.0021
ClinPred
0.35
T
GERP RS
-2.5
Varity_R
0.20
gMVP
0.33

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs200806311; hg19: chr8-71619374; API