NM_001113491.2(SEPTIN9):c.316C>T (p.Arg106Trp) AND Inborn genetic diseases

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 13, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV004018574.2

Allele description [Variation Report for NM_001113491.2(SEPTIN9):c.316C>T (p.Arg106Trp)]

NM_001113491.2(SEPTIN9):c.316C>T (p.Arg106Trp)

Gene:

SEPTIN9:septin 9 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q25.3

Genomic location:

Preferred name:

NM_001113491.2(SEPTIN9):c.316C>T (p.Arg106Trp)

HGVS:

NC_000017.11:g.77402298C>T
NG_011683.2:g.125889C>T
NM_001113491.2:c.316C>TMANE SELECT
NM_001113492.2:c.-177C>T
NM_001113493.2:c.295C>T
NM_001113494.1:c.-177C>T
NM_001293695.2:c.259C>T
NM_006640.5:c.262C>T
NP_001106963.1:p.Arg106Trp
NP_001106965.1:p.Arg99Trp
NP_001280624.1:p.Arg87Trp
NP_006631.2:p.Arg88Trp
NP_006631.2:p.Arg88Trp
LRG_370t1:c.262C>T
LRG_370t2:c.316C>T
LRG_370:g.125889C>T
LRG_370p1:p.Arg88Trp
LRG_370p2:p.Arg106Trp
NC_000017.10:g.75398380C>T
NG_011683.1:g.125889C>T
NM_001113491.1:c.316C>T
NM_006640.4:c.262C>T
p.ARG106TRP

Protein change:

R106W; ARG88TRP

Links:

OMIM: 604061.0001; dbSNP: rs80338761

NCBI 1000 Genomes Browser:

rs80338761

Molecular consequence:

NM_001113492.2:c.-177C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001113494.1:c.-177C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001113491.2:c.316C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001113493.2:c.295C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001293695.2:c.259C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_006640.5:c.262C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004947200	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Dec 13, 2022)	germline	clinical testing	PubMed (9) [See all records that cite these PMIDs] 16186812, 17546647, 18492087, 19204161, 19451530, 20019224, 22981636, 28503616, 31619932 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004947200

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Dec 13, 2022)

germline

clinical testing

PubMed (9)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations in SEPT9 cause hereditary neuralgic amyotrophy.

Kuhlenbäumer G, Hannibal MC, Nelis E, Schirmacher A, Verpoorten N, Meuleman J, Watts GD, De Vriendt E, Young P, Stögbauer F, Halfter H, Irobi J, Goossens D, Del-Favero J, Betz BG, Hor H, Kurlemann G, Bird TD, Airaksinen E, Mononen T, Serradell AP, Prats JM, et al.

Nat Genet. 2005 Oct;37(10):1044-6. Epub 2005 Sep 25.

PubMed [citation]

PMID:: 16186812

SEPT9 sequence alternations causing hereditary neuralgic amyotrophy are associated with altered interactions with SEPT4/SEPT11 and resistance to Rho/Rhotekin-signaling.

Sudo K, Ito H, Iwamoto I, Morishita R, Asano T, Nagata K.

Hum Mutat. 2007 Oct;28(10):1005-13.

PubMed [citation]

PMID:: 17546647

See all PubMed Citations (9)

Details of each submission

From Ambry Genetics, SCV004947200.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (9)

Description

The c.262C>T (p.R88W) alteration is located in coding exon 2 of the SEPT9 gene. This alteration results from a C to T substitution at nucleotide position 262, causing the arginine (R) at amino acid position 88 to be replaced by a tryptophan (W). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This alteration has been reported in multiple families with hereditary neuralgic amyotrophy (Kuhlenbäumer, 2005; Laccone, 2008; Hannibal, 2009; Klein, 2009; Ueda, 2010; Leshinsky-Silver, 2013; Chuk, 2016; Serin, 2019). This amino acid position is highly conserved in available vertebrate species. Functional analysis demonstrated that the p.R88W alteration alters the interaction of septin-9 with partner molecules (Sudo, 2007). The in silico prediction for this alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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