rs191011663

Variant summary

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

The NM_001368771.2(SEPTIN4):​c.2929G>C​(p.Glu977Gln) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)

Consequence

SEPTIN4
NM_001368771.2 missense, splice_region

Scores

4
11
4
Splicing: ADA: 0.002104
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.84
Variant links:
Genes affected
SEPTIN4 (HGNC:9165): (septin 4) This gene is a member of the septin family of nucleotide binding proteins, originally described in yeast as cell division cycle regulatory proteins. Septins are highly conserved in yeast, Drosophila, and mouse, and appear to regulate cytoskeletal organization. Disruption of septin function disturbs cytokinesis and results in large multinucleate or polyploid cells. This gene is highly expressed in brain and heart. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. One of the isoforms (known as ARTS) is distinct; it is localized to the mitochondria, and has a role in apoptosis and cancer. [provided by RefSeq, Nov 2010]
SEPTIN4-AS1 (HGNC:51345): (SEPTIN4 antisense RNA 1)

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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
SEPTIN4NM_001368771.2 linkc.2929G>C p.Glu977Gln missense_variant, splice_region_variant Exon 13 of 14 ENST00000672673.2 NP_001355700.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SEPTIN4ENST00000672673.2 linkc.2929G>C p.Glu977Gln missense_variant, splice_region_variant Exon 13 of 14 NM_001368771.2 ENSP00000500383.1 O43236-7

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
31
Bravo
AF:
0.0000113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.87
BayesDel_addAF
Uncertain
0.12
D
BayesDel_noAF
Uncertain
-0.070
CADD
Pathogenic
26
DANN
Benign
0.95
DEOGEN2
Uncertain
0.60
.;.;D;.;T;.;.
Eigen
Pathogenic
0.91
Eigen_PC
Pathogenic
0.88
FATHMM_MKL
Uncertain
0.97
D
LIST_S2
Uncertain
0.95
D;D;D;D;D;.;D
M_CAP
Benign
0.044
D
MetaRNN
Uncertain
0.64
D;D;D;D;D;D;D
MetaSVM
Uncertain
-0.25
T
MutationAssessor
Pathogenic
3.2
.;.;M;.;.;.;.
PrimateAI
Uncertain
0.62
T
PROVEAN
Uncertain
-2.5
N;.;N;.;.;N;N
REVEL
Benign
0.21
Sift
Uncertain
0.0040
D;.;D;.;.;D;D
Sift4G
Uncertain
0.0050
D;T;D;D;T;D;D
Polyphen
1.0
D;D;D;D;.;D;D
Vest4
0.66
MutPred
0.28
.;.;Gain of helix (P = 0.0199);.;.;.;.;
MVP
0.92
MPC
1.3
ClinPred
0.98
D
GERP RS
5.6
Varity_R
0.47
gMVP
0.72

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.0021
dbscSNV1_RF
Benign
0.050
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: rs191011663; hg19: chr17-56598106; API