rs80338762
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_001113491.2(SEPTIN9):c.332C>T(p.Ser111Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
SEPTIN9
NM_001113491.2 missense
NM_001113491.2 missense
Scores
5
6
3
Clinical Significance
Conservation
PhyloP100: 7.40
Genes affected
SEPTIN9 (HGNC:7323): (septin 9) This gene is a member of the septin family involved in cytokinesis and cell cycle control. This gene is a candidate for the ovarian tumor suppressor gene. Mutations in this gene cause hereditary neuralgic amyotrophy, also known as neuritis with brachial predilection. A chromosomal translocation involving this gene on chromosome 17 and the MLL gene on chromosome 11 results in acute myelomonocytic leukemia. Multiple alternatively spliced transcript variants encoding different isoforms have been described.[provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 17-77402314-C-T is Pathogenic according to our data. Variant chr17-77402314-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 5864.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr17-77402314-C-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEPTIN9 | NM_001113491.2 | c.332C>T | p.Ser111Phe | missense_variant | 3/12 | ENST00000427177.6 | |
SEPTIN9 | NM_006640.5 | c.278C>T | p.Ser93Phe | missense_variant | 2/11 | ENST00000329047.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEPTIN9 | ENST00000427177.6 | c.332C>T | p.Ser111Phe | missense_variant | 3/12 | 1 | NM_001113491.2 | A1 | |
SEPTIN9 | ENST00000329047.13 | c.278C>T | p.Ser93Phe | missense_variant | 2/11 | 1 | NM_006640.5 | P3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Amyotrophic neuralgia Pathogenic:1Other:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 19, 2009 | - - |
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;.;D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D;D;D;D;D
MetaSVM
Benign
T
MutationTaster
Benign
A;A;A;A;A;A;A;A;A;A
PrimateAI
Uncertain
T
Sift4G
Uncertain
D;D;D;D;D;D;D;D
Polyphen
1.0
.;D;D;D;D;.;D;.
Vest4
0.91, 0.90, 0.93, 0.94, 0.89
MutPred
0.59
.;Gain of catalytic residue at S111 (P = 0.007);.;.;.;.;.;.;
MVP
MPC
0.51
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at