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GeneBe

10-16593417-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PM2_Supporting

The NM_012425.4(RSU1):c.811C>A(p.Pro271Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

RSU1
NM_012425.4 missense

Scores

1
7
9

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 9.60

Links

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 32.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RSU1NM_012425.4 linkuse as main transcriptc.811C>A p.Pro271Thr missense_variant 9/9 ENST00000345264.10
RSU1NM_152724.3 linkuse as main transcriptc.652C>A p.Pro218Thr missense_variant 8/8
RSU1XM_047425617.1 linkuse as main transcriptc.678C>A p.Asn226Lys missense_variant 7/7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RSU1ENST00000345264.10 linkuse as main transcriptc.811C>A p.Pro271Thr missense_variant 9/91 NM_012425.4 P1Q15404-1

Frequencies

GnomAD3 genomes
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJul 12, 2023The c.811C>A (p.P271T) alteration is located in exon 9 (coding exon 8) of the RSU1 gene. This alteration results from a C to A substitution at nucleotide position 811, causing the proline (P) at amino acid position 271 to be replaced by a threonine (T). 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
0.16
BayesDel_addAF
Uncertain
0.072
D
BayesDel_noAF
Benign
-0.13
Cadd
Uncertain
25
Dann
Uncertain
0.98
DEOGEN2
Benign
0.018
T;T;.
Eigen
Uncertain
0.54
Eigen_PC
Uncertain
0.62
FATHMM_MKL
Pathogenic
0.99
D
M_CAP
Benign
0.021
T
MetaRNN
Uncertain
0.51
D;D;D
MetaSVM
Benign
-0.97
T
MutationTaster
Benign
1.0
D;D
PrimateAI
Uncertain
0.69
T
PROVEAN
Benign
-0.68
N;N;.
REVEL
Benign
0.25
Sift
Uncertain
0.010
D;D;.
Sift4G
Benign
0.35
T;T;.
Polyphen
0.98
D;D;.
Vest4
0.65
MutPred
0.22
Gain of phosphorylation at P271 (P = 0.0123);Gain of phosphorylation at P271 (P = 0.0123);.;
MVP
0.71
MPC
0.39
ClinPred
0.98
D
GERP RS
5.2
Varity_R
0.19
gMVP
0.59

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: chr10-16635416; API