rs766657064

Variant summary

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

The NM_032376.4(TMEM101):​c.686G>C​(p.Arg229Pro) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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. R229Q) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

TMEM101
NM_032376.4 missense

Scores

4
9
6

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.05
Variant links:
Genes affected
TMEM101 (HGNC:28653): (transmembrane protein 101) Involved in positive regulation of I-kappaB kinase/NF-kappaB signaling. Predicted to be integral component of 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 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
TMEM101NM_032376.4 linkc.686G>C p.Arg229Pro missense_variant Exon 4 of 4 ENST00000206380.8 NP_115752.1 Q96IK0
TMEM101NM_001304813.2 linkc.512G>C p.Arg171Pro missense_variant Exon 5 of 5 NP_001291742.1 Q96IK0B4DFS4
TMEM101NM_001304814.2 linkc.512G>C p.Arg171Pro missense_variant Exon 5 of 5 NP_001291743.1 Q96IK0B4DFS4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TMEM101ENST00000206380.8 linkc.686G>C p.Arg229Pro missense_variant Exon 4 of 4 1 NM_032376.4 ENSP00000206380.3 Q96IK0
TMEM101ENST00000589334.5 linkc.686G>C p.Arg229Pro missense_variant Exon 5 of 5 5 ENSP00000468025.1 Q96IK0

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.76
BayesDel_addAF
Pathogenic
0.28
D
BayesDel_noAF
Pathogenic
0.16
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.24
T;T
Eigen
Uncertain
0.26
Eigen_PC
Uncertain
0.39
FATHMM_MKL
Uncertain
0.95
D
LIST_S2
Uncertain
0.90
.;D
M_CAP
Benign
0.0086
T
MetaRNN
Uncertain
0.69
D;D
MetaSVM
Benign
-0.83
T
MutationAssessor
Benign
1.0
L;L
PrimateAI
Uncertain
0.57
T
PROVEAN
Pathogenic
-4.5
.;D
REVEL
Uncertain
0.31
Sift
Uncertain
0.015
.;D
Sift4G
Benign
0.068
T;T
Polyphen
0.61
P;P
Vest4
0.73
MutPred
0.47
Gain of loop (P = 0.0435);Gain of loop (P = 0.0435);
MVP
0.31
MPC
0.65
ClinPred
0.98
D
GERP RS
5.6
Varity_R
0.84
gMVP
0.89

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: rs766657064; hg19: chr17-42089384; API