rs77962945

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_014962.4(BTBD3):​c.1394C>G​(p.Thr465Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts 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. T465I) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

BTBD3
NM_014962.4 missense

Scores

1
8
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.91
Variant links:
Genes affected
BTBD3 (HGNC:15854): (BTB domain containing 3) Enables identical protein binding activity. Predicted to be involved in cerebral cortex development and dendrite morphogenesis. Predicted to be located in nucleus. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.40981692).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BTBD3NM_014962.4 linkc.1394C>G p.Thr465Ser missense_variant Exon 4 of 4 ENST00000378226.7 NP_055777.1 Q9Y2F9-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BTBD3ENST00000378226.7 linkc.1394C>G p.Thr465Ser missense_variant Exon 4 of 4 1 NM_014962.4 ENSP00000367471.2 Q9Y2F9-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Pathogenic
0.21
D
BayesDel_noAF
Uncertain
0.060
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.050
.;.;T;.;T;.
Eigen
Uncertain
0.21
Eigen_PC
Uncertain
0.41
FATHMM_MKL
Uncertain
0.97
D
LIST_S2
Uncertain
0.93
.;.;.;.;D;D
M_CAP
Benign
0.026
D
MetaRNN
Benign
0.41
T;T;T;T;T;T
MetaSVM
Benign
-0.60
T
MutationAssessor
Benign
1.4
.;.;L;.;L;.
PrimateAI
Uncertain
0.75
T
PROVEAN
Benign
-1.5
N;N;N;.;N;.
REVEL
Uncertain
0.36
Sift
Benign
0.077
T;T;T;.;T;.
Sift4G
Benign
0.10
T;T;T;T;T;T
Polyphen
0.037
.;.;B;.;B;.
Vest4
0.47
MutPred
0.52
.;.;Gain of sheet (P = 0.0827);.;Gain of sheet (P = 0.0827);.;
MVP
0.89
MPC
0.65
ClinPred
0.66
D
GERP RS
6.0
Varity_R
0.20
gMVP
0.15

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: rs77962945; hg19: chr20-11904139; API