Global Variome shared LOVD
SCN9A (sodium channel, voltage-gated, type IX, alph...)
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Global Variome, with Curator vacancy
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Unique variants in the SCN9A gene
The variants shown are described using the NM_002977.3 transcript reference sequence.
Legend
Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column's header and hold it still. Below, a more detailed description is shown per column.
Effect
: The variant's effect on the function of the gene/protein, displayed in the format 'R/C'. R is the value reported by the source (publication, submitter) and this classification may vary between records. C is the value concluded by the curator. Note that in some database the curator uses Summary records to give details on the classification of the variant.Values used: '+' indicating the variant affects function, '+?' probably affects function, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect was not classified.
Reported
: The number of times this variant has been reported in the database.
Exon
: number of exon/intron containing variant; 2 = exon 2, 12i = intron 12, 2i_7i = from intron 2 to intron 7, 8i_9 = intron 8/exon 9 boundary, _1 = 5' to exon 1, 18_ = 3' of exon 18, _1_18_ = encompassing the entire 18-exon gene
DNA change (cDNA)
: description of variant at DNA level, based on a coding DNA reference sequence (following HGVS recommendations); e.g. c.123C>T, c.123_145del, c.123_126dup. For deletions/duplications extending beyond the reference transcript resp. {0}/{2} is used to replace del/dup. Extent of the deletion/duplication should be specified using the genomic description (g.). "-" indicates the variant described on genomic level does not affect the coding DNA reference sequence.
RNA change
: description of variant at RNA level (following HGVS recommendations).
r.123c>u
r.? = unknown
r.(?) = RNA not analysed but probably transcribed copy of DNA variant
r.spl? = RNA not analysed but variant probably affects splicing
r.(spl?) = RNA not analysed but variant may affect splicing
r.0? = change expected to abolish transcription
Protein
: description of variant at protein level (following HGVS recommendations).
p.(Arg345Pro) = change predicted from DNA (RNA not analysed)
p.Arg345Pro = change derived from RNA analysis
p.? = unknown effect
p.0? = probably no protein produced
P-domain
: region/domain protein affected
Classification method
: The method used for the clinical classification of this variant.
All options:
ACMG
ACGS
EAHAD-CFDB
ENIGMA
InSiGHT
kConFab
other
Clinical classification
: Clinical classification of variant, preferably based on standardised criteria (e.g. ACMG), directed on the clinical consequences as published/submitted, indicated using an enriched system including inheritance: e.g. pathogenic, pathogenic (dominant), pathogenic (recessive), pathogenic (!), pathogenic (maternal), pathogenic (paternal). Standard inheritance is covered by dominant/recessive, sex-linked and imprinting by maternal/paternal. A '!' warns for exceptional circumstances to be explained in the 'Remarks' field (low penetrance, variants pathogenic in heterozygous state only, hypomorphic/hypermorphic variants, protective variants, etc.). Non-disease consequences (e.g. drug metabolism (pharmacogenetics), risk factor, blood group, tasting bitter) are indicated using additions to the benign classification; benign (dominant), benign (recessive), benign (!), etc. The value 'association' is used for variants associated with a phenotype and 'NA' for variants from in vitro/in silico records. NOTE: classification may differ from the opinion of the curator as given in a variant SUMMARY-record or the 'Functional effect concluded'). NOTE: pathogenic/likely pathogenic should go together with "variant (probably) affects function" In ClassFunctional.
All options:
pathogenic
pathogenic (dominant)
pathogenic (recessive)
pathogenic (!)
pathogenic (maternal)
pathogenic (paternal)
likely pathogenic
likely pathogenic (dominant)
likely pathogenic (recessive)
likely pathogenic (!)
likely pathogenic (maternal)
likely pathogenic (paternal)
VUS
VUS (!)
likely benign
likely benign (dominant)
likely benign (recessive)
likely benign (!)
likely benign (maternal)
likely benign (paternal)
benign
benign (dominant)
benign (recessive)
benign (!)
benign (maternal)
benign (paternal)
association
unclassified
NA
DNA change (genomic) (hg19)
: HGVS description of variant at DNA level, based on the genomic (chromosomal) DNA reference sequence; e.g. g.12345678C>T, g.12345679del, g.12345678_12345890dup
DNA change (hg38)
: HGVS description of variant at DNA level, based on the hg38 genomic (chromosomal) eference sequence; e.g. g.12345678C>T, g.12345679del, g.12345678_12345890dup
Published as
: listed only when different from "DNA change"; variant as reported originally (e.g. 521delT). Variants seen in animal models, tested in vitro, predicted from RNA analysis, etc. are described between brackets like c.(456C>G)
ISCN
: description of the variant according to ISCN nomenclature
DB-ID
: database ID of variant, grouping multiple observations of the same variant together, starting with the HGNC gene symbol, followed by an underscore (_) and a six digit number (e.g. DMD_012345). _000000 is used for variants where DNA was not analysed (change predicted from RNA analysis), variants seen in animal models or variants not seen in humans but functionally tested in vitro
Variant remarks
: remarks regarding variant described, e.g. germline mosaicism in mother, 345 kb deletion, muscle RNA analysed, not in 200 control chromosomes tested, on founder haplotype, etc.
Reference
: publication describing the variant submitted, incl. links to OMIM, PubMed or other source, e.g. "den Dunnen ASHG2003 P2346"
ClinVar ID
: ID of variant in ClinVar database
dbSNP ID
: the dbSNP ID
Origin
: Origin of variant/record: Germline = in all cells, De novo = in all cells, but not in either parent, Germline/De novo (untested) = in all cells, parents not tested (use only when De novo is likely, e.g. isolated/sporadic cases with dominant disease), Somatic = present in a subset of cells, but not in either parent, Uniparental disomy = from parental disomy (maternal or paternal), CLASSIFICATION record = submitter only sharing variant classification (note another report may share Individual data), SUMMARY record = master summary record from curator (may link to another database), In vitro (cloned) = data resulting from in vitro functional assays, animal model = data from animal model, Artefact = false positive variant call, DUPLICATE record = variant already described on another chromosome (e.g. unbalanced translocation, duplicating transposition, 2nd fusion transcript, etc.)
All options:
Germline
De novo
Germline/De novo (untested)
Somatic
Uniparental disomy
Uniparental disomy, maternal allele
Uniparental disomy, paternal allele
CLASSIFICATION record
SUMMARY record
In vitro (cloned)
In silico
animal model
Artefact
DUPLICATE record
Unknown
Not applicable
Segregation
: Indicates whether the variant segregates with the phenotype (yes), does not segregate with the phenotype (no) or segregation is unknown (?)
All options:
? = unknown
yes = segregates with phenotype
no = does not segregate with phenotype
- = not applicable
Frequency
: frequency in which the variant was found; e.g 5/760 chromosomes (in 5 of 760 chromosomes tested), 1/33 patients (in 1 of 33 patients analysed in study), 0.05 controls (in 5% of control cases tested)
Re-site
: restriction enzyme recognition site created (+) or destroyed (-); e.g. BglII+, BamHI-
VIP
: variant VIP-status was requested for matchmaking - need collaboration(s) to crack the case - please contact the submitter/curator. NOTE: to get VIP status ask the curator.
Methylation
: result of methylation test; GOM (gain of methylation), LOM (loss of methylation), 30% (30% methylated). NOTE: when several tests were done mention the method as well (e.g. MS-PCR 75%)
How to query this table
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Operator
Column type
Example
Matches
Text
Arg
all entries containing 'Arg'
space
Text
Arg Ser
all entries containing 'Arg' and 'Ser'
|
Text
Arg|Ser
all entries containing 'Arg' or 'Ser'
!
Text
!fs
all entries not containing 'fs'
^
Text
^p.(Arg
all entries beginning with 'p.(Arg'
$
Text
Ser)$
all entries ending with 'Ser)'
=""
Text
=""
all entries with this field empty
=""
Text
="p.0"
all entries exactly matching 'p.0'
!=""
Text
!=""
all entries with this field not empty
!=""
Text
!="p.0"
all entries not exactly matching 'p.0?'
combination
Text
*|Ter !fs
all entries containing '*' or 'Ter' but not containing 'fs'
Date
2020
all entries matching the year 2020
|
Date
2020-03|2020-04
all entries matching March or April, 2020
!
Date
!2020-03
all entries not matching March, 2020
<
Date
<2020
all entries before the year 2020
<=
Date
<=2020-06
all entries in or before June, 2020
>
Date
>2020-06
all entries after June, 2020
>=
Date
>=2020-06-15
all entries on or after June 15th, 2020
combination
Date
2019|2020 <2020-03
all entries in 2019 or 2020, and before March, 2020
Numeric
23
all entries exactly matching 23
|
Numeric
23|24
all entries exactly matching 23 or 24
!
Numeric
!23
all entries not exactly matching 23
<
Numeric
<23
all entries lower than 23
<=
Numeric
<=23
all entries lower than, or equal to, 23
>
Numeric
>23
all entries higher than 23
>=
Numeric
>=23
all entries higher than, or equal to, 23
combination
Numeric
>=20 <30 !23
all entries with values from 20 to 29, but not equal to 23
Some more advanced examples:
Example
Matches
Asian
all entries containing 'Asian', 'asian', including 'Caucasian', 'caucasian', etc.
Asian !Caucasian
all entries containing 'Asian' but not containing 'Caucasian'
Asian|African !Caucasian
all entries containing 'Asian' or 'African', but not containing 'Caucasian'
"South Asian"
all entries containing 'South Asian', but not containing 'South East Asian'
To sort on a certain column, click on the column header or on the arrows. If that column is already selected to sort on, the sort order will be swapped. The column currently sorted on has a darker blue background color than the other columns. The up and down arrows next to the column name indicate the current sorting direction. When sorting on any field other than the default, LOVD will sort secondarily on the default sort column.
265 entries on 3 pages. Showing entries 1 - 100.
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Effect
Reported
Exon
DNA change (cDNA)
RNA change
Protein
P-domain
Classification method
Clinical classification
DNA change (genomic) (hg19)
DNA change (hg38)
Published as
ISCN
DB-ID
Variant remarks
Reference
ClinVar ID
dbSNP ID
Origin
Segregation
Frequency
Re-site
VIP
Methylation
Owner
?/.
1
-
c.20C>T
r.(?)
p.(Pro7Leu)
-
-
VUS
g.167168247G>A
g.166311737G>A
SCN9A(NM_002977.3):c.20C>T (p.P7L)
-
SCN9A_000153
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
?/.
1
-
c.77G>C
r.(?)
p.(Arg26Pro)
-
-
VUS
g.167168190C>G
g.166311680C>G
-
-
SCN9A_000249
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
?/.
1
-
c.77G>T
r.(?)
p.(Arg26Leu)
-
-
VUS
g.167168190C>A
g.166311680C>A
-
-
SCN9A_000238
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
?/.
1
-
c.118A>G
r.(?)
p.(Lys40Glu)
-
-
VUS
g.167168149T>C
g.166311639T>C
-
-
SCN9A_000237
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-?/.
3
-
c.129T>C
r.(?)
p.(Asp43=)
-
-
likely benign
g.167168138A>G
g.166311628A>G
SCN9A(NM_002977.3):c.129T>C (p.D43=, p.=)
-
SCN9A_000170
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
,
VKGL-NL_Nijmegen
,
VKGL-NL_AMC
+/., -/.
5
2
c.174G>A
r.(=), r.(?)
p.(=), p.(Gln58=)
N-terminus
-
benign, pathogenic
g.167168093C>T
g.166311583C>T
SCN9A(NM_002977.3):c.174G>A (p.Q58=)
-
SCN9A_000008
VKGL data sharing initiative Nederland
PubMed: Drenth 2005
-
rs6432901
CLASSIFICATION record, Germline
-
-
-
-
-
Andreas Laner
,
VKGL-NL_Groningen
,
VKGL-NL_Utrecht
,
VKGL-NL_AMC
,
Christoph Lossin
+/.
1
2
c.184A>G
r.(?)
p.(Ile62Val)
N-terminus
-
pathogenic
g.167168083T>C
g.166311573T>C
-
-
SCN9A_000012
-
PubMed: Singh 2009
-
-
Germline
-
-
-
-
-
Christoph Lossin
-?/.
1
-
c.204C>T
r.(?)
p.(Pro68=)
-
-
likely benign
g.167168063G>A
g.166311553G>A
-
-
SCN9A_000248
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-?/.
1
-
c.240C>T
r.(?)
p.(Pro80=)
-
-
likely benign
g.167168027G>A
g.166311517G>A
-
-
SCN9A_000268
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-?/.
1
-
c.252C>T
r.(?)
p.(Asp84=)
-
-
likely benign
g.167168015G>A
g.166311505G>A
-
-
SCN9A_000267
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-/.
1
-
c.259-79G>A
r.(=)
p.(=)
-
-
benign
g.167163663C>T
g.166307153C>T
-
-
SCN9A_000094
-
-
-
rs4447616
Germline
-
-
-
-
-
Andreas Laner
./.
1
-
c.269T>C
r.(?)
p.(Val90Ala)
-
-
VUS
g.167163574A>G
g.166307064A>G
-
-
SCN9A_000108
-
PubMed: Bobbili 2018
,
Journal: Bobbili 2018
-
-
Germline
-
1/567 controls
-
-
-
Dheeraj Bobbili
./.
1
-
c.294C>A
r.(?)
p.(Phe98Leu)
-
-
VUS
g.167163549G>T
g.166307039G>T
-
-
SCN9A_000107
-
PubMed: Bobbili 2018
,
Journal: Bobbili 2018
-
rs199824489
Germline
-
1/567 controls
-
-
-
Dheeraj Bobbili
?/.
2
-
c.361A>C
r.(?)
p.(Lys121Gln)
-
-
VUS
g.167163482T>G
g.166306972T>G
SCN9A(NM_002977.3):c.361A>C (p.K121Q)
-
SCN9A_000152
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
,
VKGL-NL_Nijmegen
?/.
1
-
c.371T>C
r.(?)
p.(Val124Ala)
-
-
VUS
g.167163472A>G
-
-
-
SCN9A_000278
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-/.
1
-
c.377+92dup
r.(=)
p.(=)
-
-
benign
g.167163375dup
g.166306865dup
SCN9A(NM_002977.3):c.377+92dupT
-
SCN9A_000151
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
-/.
2
-
c.377+93G>T
r.(=)
p.(=)
-
-
benign
g.167163373C>A
g.166306863C>A
SCN9A(NM_002977.3):c.377+93G>T
-
SCN9A_000011
VKGL data sharing initiative Nederland
-
-
rs4443015
CLASSIFICATION record, Germline
-
-
-
-
-
Andreas Laner
,
VKGL-NL_Utrecht
-/., ?/.
3
3i
c.377+94A>G
r.(=)
p.(=)
-
-
benign, VUS
g.167163372T>C
g.166306862T>C
SCN9A(NM_002977.3):c.377+94A>G
-
SCN9A_000001
VKGL data sharing initiative Nederland
Lossin, unpublished data
-
rs58349687
CLASSIFICATION record, Germline
-
-
-
-
-
Andreas Laner
,
VKGL-NL_Utrecht
,
Christoph Lossin
?/.
1
3i
c.378-90T>A
r.(=)
p.(=)
-
-
VUS
g.167163199A>T
g.166306689A>T
-
-
SCN9A_000002
-
Lossin, unpublished data
-
-
Germline
-
-
-
-
-
Christoph Lossin
+/.
1
4
c.406A>G
r.(?)
p.(Ile136Val)
D1/S1
-
pathogenic
g.167163081T>C
g.166306571T>C
-
-
SCN9A_000013
-
PubMed: Cheng 2008
-
-
Germline
-
-
-
-
-
Christoph Lossin
+/., -/.
5
2
c.444A>G
r.(=), r.(?)
p.(=), p.(Pro148=)
D1/S1-S2ex
-
benign, pathogenic
g.167163043T>C
g.166306533T>C
P148P, SCN9A(NM_002977.3):c.444A>G (p.P148=, p.=)
-
SCN9A_000009
VKGL data sharing initiative Nederland
PubMed: Drenth 2005
-
rs964677
CLASSIFICATION record, Germline
-
-
-
-
-
Andreas Laner
,
VKGL-NL_Groningen
,
VKGL-NL_Utrecht
,
VKGL-NL_AMC
,
Christoph Lossin
+/.
1
4
c.446C>A
r.(?)
p.(Pro149Gln)
D1/S1-S2ex
-
pathogenic
g.167163041G>T
g.166306531G>T
-
-
SCN9A_000014
-
PubMed: Singh 2009
-
-
Germline
-
-
-
-
-
Christoph Lossin
?/.
1
-
c.457A>C
r.(?)
p.(Lys153Gln)
-
-
VUS
g.167163030T>G
g.166306520T>G
SCN9A(NM_002977.3):c.457A>C (p.K153Q)
-
SCN9A_000266
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
1
-
c.465C>T
r.(?)
p.(Val155=)
-
-
likely benign
g.167163022G>A
g.166306512G>A
-
-
SCN9A_000236
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-/., -?/., ?/.
6
-
c.554G>A
r.(?)
p.(Arg185His)
-
-
benign, likely benign, VUS
g.167162344C>T
g.166305834C>T
SCN9A(NM_002977.3):c.554G>A (p.R185H)
-
SCN9A_000150
8 heterozygous, no homozygous;
Clinindb (India)
, VKGL data sharing initiative Nederland,
1 more item
PubMed: Le 2019
,
PubMed: Narang 2020
,
Journal: Narang 2020
-
rs73969684
CLASSIFICATION record, Germline
-
8/2795 individuals, frequency 0.023
-
-
-
Global Variome, with Curator vacancy
,
VKGL-NL_Rotterdam
,
VKGL-NL_Utrecht
,
VKGL-NL_Nijmegen
,
VKGL-NL_AMC
,
Mohammed Faruq
?/.
1
-
c.558C>A
r.(?)
p.(Asp186Glu)
-
-
VUS
g.167162340G>T
-
SCN9A(NM_002977.3):c.558C>A (p.D186E)
-
SCN9A_000290
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
-/., ?/.
2
5i
c.596+25C>T
r.(=)
p.(=)
-
-
benign, VUS
g.167162277G>A
g.166305767G>A
-
-
SCN9A_000003
-
Lossin, unpublished data
-
rs4429487
Germline
-
-
-
-
-
Andreas Laner
,
Christoph Lossin
?/.
1
-
c.599A>G
r.(?)
p.(Tyr200Cys)
-
-
VUS
g.167160837T>C
g.166304327T>C
-
-
SCN9A_000235
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/.
1
6
c.601T>G
r.(?)
p.(Leu201Val)
D1/S3
-
pathogenic
g.167160835A>C
g.166304325A>C
-
-
SCN9A_000015
-
PubMed: Hisama 2006.
-
-
Germline
-
-
-
-
-
Christoph Lossin
+/.
1
6
c.616A>G
r.(?)
p.(Asn206Asp)
D1/S3-S4ex
-
pathogenic
g.167160820T>C
g.166304310T>C
-
-
SCN9A_000016
-
PubMed: Hisama 2006.
-
-
Germline
-
-
-
-
-
Christoph Lossin
?/.
1
-
c.619C>G
r.(?)
p.(Leu207Val)
-
-
VUS
g.167160817G>C
g.166304307G>C
-
-
SCN9A_000234
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/.
1
6
c.647T>C
r.(?)
p.(Phe216Ser)
D1/S4
-
pathogenic
g.167160789A>G
g.166304279A>G
-
-
SCN9A_000017
-
PubMed: Drenth 2005
-
-
Germline
-
-
-
-
-
Christoph Lossin
-?/.
1
-
c.655T>C
r.(?)
p.(Leu219=)
-
-
likely benign
g.167160781A>G
g.166304271A>G
-
-
SCN9A_000265
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/.
1
6
c.684C>G
r.(?)
p.(Ile228Met)
D1/S4
-
pathogenic
g.167160752G>C
g.166304242G>C
-
-
SCN9A_000018
-
PubMed: Singh 2009
-
-
Germline
-
-
-
-
-
Christoph Lossin
-?/.
1
-
c.688+9T>C
r.(=)
p.(=)
-
-
likely benign
g.167160739A>G
g.166304229A>G
SCN9A(NM_002977.3):c.688+9T>C
-
SCN9A_000247
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
-/.
2
-
c.688+13T>C
r.(=)
p.(=)
-
-
benign
g.167160735A>G
g.166304225A>G
SCN9A(NM_002977.3):c.688+13T>C
-
SCN9A_000080
VKGL data sharing initiative Nederland
-
-
rs7444988
CLASSIFICATION record, Germline
-
-
-
-
-
Andreas Laner
,
VKGL-NL_AMC
?/.
1
6i
c.689-217A>G
r.(=)
p.(=)
-
-
VUS
g.167160029T>C
g.166303519T>C
-
-
SCN9A_000004
-
Lossin, unpublished data
-
-
Germline
-
-
-
-
-
Christoph Lossin
?/.
1
-
c.715A>G
r.(?)
p.(Ile239Val)
-
-
VUS
g.167159786T>C
g.166303276T>C
SCN9A(NM_002977.3):c.715A>G (p.I239V)
-
SCN9A_000149
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
1
7
c.721T>A
r.(?)
p.(Ser241Thr)
D1/S4-S5in
-
pathogenic
g.167159780A>T
g.166303270A>T
-
-
SCN9A_000019
-
PubMed: Lampert 2006
-
-
Germline
-
-
-
-
-
Christoph Lossin
+/.
1
7
c.774_775del
r.(?)
p.(Val258Valfs*16)
D1/S5
-
pathogenic
g.167159730_167159731del
g.166303220_166303221del
774_775delGT
-
SCN9A_000020
-
PubMed: Nilsen 2009
-
-
Germline
-
-
-
-
-
Christoph Lossin
?/.
1
-
c.796C>A
r.(?)
p.(Leu266Met)
-
-
VUS
g.167159705G>T
g.166303195G>T
-
-
SCN9A_000264
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-?/.
1
-
c.817C>T
r.(?)
p.(His273Tyr)
-
-
likely benign
g.167159684G>A
-
-
-
SCN9A_000289
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-?/.
1
-
c.829C>A
r.(?)
p.(Arg277=)
-
-
likely benign
g.167159672G>T
-
-
-
SCN9A_000288
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/.
1
7
c.829C>T
r.(?)
p.(Arg277*)
P1
-
pathogenic
g.167159672G>A
g.166303162G>A
-
-
SCN9A_000021
-
PubMed: Goldberg 2007
-
-
Germline
-
-
-
-
-
Christoph Lossin
-?/.
1
-
c.876C>T
r.(?)
p.(Thr292=)
-
-
likely benign
g.167159625G>A
g.166303115G>A
-
-
SCN9A_000233
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-?/.
1
-
c.965+13T>C
r.(=)
p.(=)
-
-
likely benign
g.167151096A>G
g.166294586A>G
-
-
SCN9A_000232
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-?/.
2
-
c.966-8G>A
r.(=)
p.(=)
-
-
likely benign
g.167149890C>T
g.166293380C>T
SCN9A(NM_002977.3):c.966-8G>A
-
SCN9A_000231
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
,
VKGL-NL_AMC
+/.
1
9
c.984C>A
r.(?)
p.(Tyr328*)
P1
-
pathogenic
g.167149864G>T
g.166293354G>T
-
-
SCN9A_000022
-
PubMed: Goldberg 2007
-
-
Germline
-
-
-
-
-
Christoph Lossin
?/.
1
-
c.1007A>C
r.(?)
p.(Asn336Thr)
-
-
VUS
g.167149841T>G
g.166293331T>G
-
-
SCN9A_000230
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-/.
1
-
c.1107+41A>G
r.(=)
p.(=)
-
-
benign
g.167149700T>C
g.166293190T>C
-
-
SCN9A_000079
-
-
-
rs41268675
Germline
-
-
-
-
-
Andreas Laner
-/.
1
-
c.1107+48C>T
r.(=)
p.(=)
-
-
benign
g.167149693G>A
g.166293183G>A
-
-
SCN9A_000078
-
-
-
rs7588632
Germline
-
-
-
-
-
Andreas Laner
?/.
1
-
c.1109C>T
r.(?)
p.(Thr370Met)
-
-
VUS
g.167145152G>A
g.166288642G>A
-
-
SCN9A_000251
1 heterozygous, no homozygous;
Clinindb (India)
PubMed: Narang 2020
,
Journal: Narang 2020
-
rs200391162
Germline
-
1/2794 individuals
-
-
-
Mohammed Faruq
-/., -?/.
2
-
c.1110G>A
r.(?)
p.(Thr370=)
-
-
benign, likely benign
g.167145151C>T
g.166288641C>T
SCN9A(NM_002977.3):c.1110G>A (p.T370=)
-
SCN9A_000148
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
,
VKGL-NL_AMC
-/., ?/.
4
10
c.1119T>C
r.(=), r.(?)
p.(=), p.(Ala373=)
P1
-
benign, VUS
g.167145142A>G
g.166288632A>G
A373A, SCN1A-AS1(NR_110260.1):n.1030-5933A>G, SCN9A(NM_002977.3):c.1119T>C (p.A373=)
-
SCN9A_000023
VKGL data sharing initiative Nederland
PubMed: Drenth 2005
-
rs13414203
CLASSIFICATION record, Germline
-
-
-
-
-
Andreas Laner
,
VKGL-NL_Groningen
,
VKGL-NL_AMC
,
Christoph Lossin
?/.
1
-
c.1143_1145del
r.(?)
p.(Phe382del)
-
-
VUS
g.167145120_167145122del
g.166288610_166288612del
-
-
SCN9A_000076
-
-
-
-
Germline
-
-
-
-
-
Andreas Laner
-/.
3
-
c.1155G>T
r.(?)
p.(Val385=)
-
-
benign
g.167145106C>A
g.166288596C>A
SCN9A(NM_002977.3):c.1155G>T (p.V385=)
-
SCN9A_000147
VKGL data sharing initiative Nederland
-
-
rs58465962
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
,
VKGL-NL_Nijmegen
,
VKGL-NL_AMC
-?/.
1
-
c.1177C>T
r.(?)
p.(Leu393=)
-
-
likely benign
g.167145084G>A
g.166288574G>A
-
-
SCN9A_000263
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/.
1
10
c.1185C>A
r.(?)
p.(Asn395Lys)
D1/S6
-
pathogenic
g.167145076G>T
g.166288566G>T
N395K
-
SCN9A_000024
-
PubMed: Drenth 2005
-
-
Germline
-
-
-
-
-
Christoph Lossin
-/., ?/.
4
10
c.1266A>G
r.(=), r.(?)
p.(=), p.(Glu422=)
L1
-
benign, VUS
g.167144995T>C
g.166288485T>C
E422E, SCN1A-AS1(NR_110260.1):n.1030-6080T>C, SCN9A(NM_002977.3):c.1266A>G (p.E422=)
-
SCN9A_000025
VKGL data sharing initiative Nederland
PubMed: Drenth 2005
-
rs13402180
CLASSIFICATION record, Germline
-
-
-
-
-
Andreas Laner
,
VKGL-NL_Groningen
,
VKGL-NL_AMC
,
Christoph Lossin
-/., ?/.
4
10
c.1287T>A
r.(=), r.(?)
p.(=), p.(Arg429=)
L1
-
benign, VUS
g.167144974A>T
g.166288464A>T
R429R, SCN1A-AS1(NR_110260.1):n.1030-6101A>T, SCN9A(NM_002977.3):c.1287T>A (p.R429=)
-
SCN9A_000026
VKGL data sharing initiative Nederland
PubMed: Drenth 2005
-
rs6747673
CLASSIFICATION record, Germline
-
-
-
-
-
Andreas Laner
,
VKGL-NL_Groningen
,
VKGL-NL_AMC
,
Christoph Lossin
?/.
1
-
c.1314+3A>T
r.spl?
p.?
-
-
VUS
g.167144944T>A
-
-
-
SCN9A_000287
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
?/.
1
-
c.1318A>G
r.(?)
p.(Ile440Val)
-
-
VUS
g.167143130T>C
g.166286620T>C
SCN9A(NM_002977.3):c.1318A>G (p.I440V)
-
SCN9A_000262
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
-?/.
1
-
c.1326G>A
r.(?)
p.(Ala442=)
-
-
likely benign
g.167143122C>T
g.166286612C>T
-
-
SCN9A_000261
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-?/.
1
-
c.1331C>T
r.(?)
p.(Ala444Val)
-
-
likely benign
g.167143117G>A
g.166286607G>A
-
-
SCN9A_000246
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
?/.
1
-
c.1348A>G
r.(?)
p.(Ile450Val)
-
-
VUS
g.167143100T>C
g.166286590T>C
-
-
SCN9A_000158
-
-
-
-
Germline
-
-
-
-
-
Andreas Laner
+/.
3
11
c.1376C>G
r.(?)
p.(Ser459*)
L1
-
pathogenic, pathogenic (recessive)
g.167143072G>C
g.166286562G>C
S459X
-
SCN9A_000027
-
PubMed: Antoniadi 2015
,
PubMed: Cox 2006
-
rs121908908
Germline
-
-
-
-
-
Johan den Dunnen
,
Christoph Lossin
-?/.
3
-
c.1398C>T
r.(?)
p.(Ser466=)
-
-
likely benign
g.167143050G>A
g.166286540G>A
SCN9A(NM_002977.3):c.1398C>T (p.S466=, p.=)
-
SCN9A_000146
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
,
VKGL-NL_Utrecht
,
VKGL-NL_Nijmegen
-?/.
2
-
c.1464C>T
r.(?)
p.(Leu488=)
-
-
likely benign
g.167142984G>A
g.166286474G>A
SCN9A(NM_002977.3):c.1464C>T (p.L488=)
-
SCN9A_000229
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
,
VKGL-NL_AMC
+/., -/.
5
11
c.1469G>A
r.(?)
p.(Ser490Asn)
L1
-
benign, pathogenic
g.167142979C>T
g.166286469C>T
SCN9A(NM_002977.3):c.1469G>A (p.S490N)
-
SCN9A_000028
VKGL data sharing initiative Nederland
PubMed: Singh 2009
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
VKGL-NL_Groningen
,
VKGL-NL_Utrecht
,
VKGL-NL_Nijmegen
,
VKGL-NL_AMC
,
Christoph Lossin
-?/.
1
-
c.1497A>G
r.(?)
p.(Lys499=)
-
-
likely benign
g.167142951T>C
g.166286441T>C
-
-
SCN9A_000245
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
?/.
1
-
c.1552G>T
r.(?)
p.(Val518Phe)
-
-
VUS
g.167142896C>A
g.166286386C>A
-
-
SCN9A_000228
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/., ./., ?/.
3
11
c.1555G>A
r.(?)
p.(Glu519Lys)
L1
-
pathogenic, VUS
g.167142893C>T
g.166286383C>T
-
-
SCN9A_000029
VKGL data sharing initiative Nederland
PubMed: Bobbili 2018
,
Journal: Bobbili 2018
,
PubMed: Singh 2009
-
rs187453572
CLASSIFICATION record, Germline
-
1/567 controls
-
-
-
Dheeraj Bobbili
,
VKGL-NL_Nijmegen
,
Christoph Lossin
?/.
1
-
c.1592C>A
r.(?)
p.(Thr531Asn)
-
-
VUS
g.167142856G>T
g.166286346G>T
-
-
SCN9A_000227
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
?/.
1
-
c.1602+55T>G
r.(=)
p.(=)
-
-
VUS
g.167142791A>C
g.166286281A>C
-
-
SCN9A_000157
-
-
-
-
Germline
-
-
-
-
-
Andreas Laner
-?/.
1
-
c.1603-14T>A
r.(=)
p.(=)
-
-
likely benign
g.167141348A>T
g.166284838A>T
-
-
SCN9A_000226
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
?/.
1
-
c.1691T>C
r.(?)
p.(Ile564Thr)
-
-
VUS
g.167141246A>G
g.166284736A>G
-
-
SCN9A_000225
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-?/.
1
-
c.1804A>G
r.(?)
p.(Ile602Val)
-
-
likely benign
g.167141133T>C
g.166284623T>C
-
-
SCN9A_000224
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/., -/., -?/.
7
12
c.1828C>A
r.(?)
p.(Pro610Thr)
L1
-
benign, likely benign, pathogenic
g.167141109G>T
g.166284599G>T
SCN9A(NM_002977.3):c.1828C>A (p.P610T)
-
SCN9A_000030
1 homozygous;
Clinindb (India)
, 60 heterozygous;
Clinindb (India)
,
1 more item
PubMed: Drenth 2005
,
PubMed: Narang 2020
,
Journal: Narang 2020
-
rs41268673
CLASSIFICATION record, Germline
-
1/2795 individuals, 60/2795 individuals
-
-
-
Andreas Laner
,
VKGL-NL_Utrecht
,
VKGL-NL_Nijmegen
,
VKGL-NL_AMC
,
Christoph Lossin
,
Mohammed Faruq
-?/.
1
-
c.1838C>T
r.(?)
p.(Pro613Leu)
-
-
likely benign
g.167141099G>A
g.166284589G>A
-
-
SCN9A_000223
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/., ./.
2
12
c.1846G>A
r.(?)
p.(Gly616Arg)
L1
-
pathogenic, VUS
g.167141091C>T
g.166284581C>T
-
-
SCN9A_000031
-
PubMed: Bobbili 2018
,
Journal: Bobbili 2018
,
PubMed: Choi 2010
-
rs201338643
Germline
-
1/194 cases RE
-
-
-
Dheeraj Bobbili
,
Christoph Lossin
+?/.
1
-
c.1867G>A
r.(?)
p.(Asp623Asn)
-
-
likely pathogenic
g.167141070C>T
g.166284560C>T
-
-
SCN9A_000222
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-?/.
1
-
c.1875C>T
r.(?)
p.(Asn625=)
-
-
likely benign
g.167141062G>A
g.166284552G>A
-
-
SCN9A_000260
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-?/.
1
-
c.1881G>A
r.(?)
p.(Val627=)
-
-
likely benign
g.167141056C>T
g.166284546C>T
SCN9A(NM_002977.3):c.1881G>A (p.V627=)
-
SCN9A_000221
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
-?/.
1
-
c.1901G>A
r.(?)
p.(Arg634His)
-
-
likely benign
g.167141036C>T
g.166284526C>T
-
-
SCN9A_000220
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/.
1
12
c.1921A>T
r.(?)
p.(Asn641Tyr)
L1
-
pathogenic
g.167141016T>A
g.166284506T>A
-
-
SCN9A_000032
-
PubMed: Singh 2009
-
-
Germline
-
-
-
-
-
Christoph Lossin
-?/.
1
-
c.1941+33C>T
r.(=)
p.(=)
-
-
likely benign
g.167140963G>A
g.166284453G>A
-
-
SCN9A_000219
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-/.
1
-
c.1941+41C>T
r.(=)
p.(=)
-
-
benign
g.167140955G>A
g.166284445G>A
-
-
SCN9A_000155
-
-
-
rs7608201
Germline
-
-
-
-
-
Andreas Laner
?/.
1
-
c.1942-27T>G
r.(=)
p.(=)
-
-
VUS
g.167138345A>C
g.166281835A>C
-
-
SCN9A_000218
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-?/.
1
-
c.1942-22C>T
r.(=)
p.(=)
-
-
likely benign
g.167138340G>A
g.166281830G>A
-
-
SCN9A_000217
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-/.
1
-
c.1942-6T>A
r.(=)
p.(=)
-
-
benign
g.167138324A>T
g.166281814A>T
SCN9A(NM_002977.3):c.1942-6T>A
-
SCN9A_000169
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
-?/.
1
-
c.1942-4T>A
r.spl?
p.?
-
-
likely benign
g.167138322A>T
g.166281812A>T
SCN9A(NM_002977.3):c.1942-4T>A
-
SCN9A_000143
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
-/.
2
-
c.1942-3del
r.spl?
p.?
-
-
benign
g.167138330del
g.166281820del
SCN9A(NM_002977.3):c.1942-3delT
-
SCN9A_000142
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
,
VKGL-NL_AMC
-/., -?/.
2
-
c.1942-3dup
r.spl?
p.?
-
-
benign, likely benign
g.167138330dup
g.166281820dup
1 more item
-
SCN9A_000144
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
,
VKGL-NL_AMC
./.
1
-
c.1946C>T
r.(?)
p.(Thr649Met)
-
-
VUS
g.167138314G>A
g.166281804G>A
-
-
SCN9A_000104
-
PubMed: Bobbili 2018
,
Journal: Bobbili 2018
-
rs200965749
Germline
-
1/194 cases RE
-
-
-
Dheeraj Bobbili
-?/.
1
-
c.1947G>A
r.(?)
p.(Thr649=)
-
-
likely benign
g.167138313C>T
g.166281803C>T
-
-
SCN9A_000259
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/., -?/.
5
13
c.1964A>G
r.(?)
p.(Lys655Arg)
L1
-
likely benign, pathogenic
g.167138296T>C
g.166281786T>C
SCN9A(NM_002977.3):c.1964A>G (p.K655R)
-
SCN9A_000033
VKGL data sharing initiative Nederland
PubMed: Singh 2009
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
VKGL-NL_Utrecht
,
VKGL-NL_Nijmegen
,
VKGL-NL_AMC
,
Christoph Lossin
-?/.
1
-
c.1974T>C
r.(?)
p.(Arg658=)
-
-
likely benign
g.167138286A>G
g.166281776A>G
-
-
SCN9A_000244
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+?/.
1
-
c.2026_2029del
r.(?)
p.Gln676Glufs*3
-
ACMG
likely pathogenic
g.167138235_167138238del
g.166281725_166281728del
-
-
SCN9A_000171
no second variant deceted in SCN9A, LOF variants in SCN9A follow a recessive mode of inheritance
-
-
-
Germline
-
-
-
-
-
Andreas Laner
?/.
1
-
c.2033C>A
r.(?)
p.(Ala678Glu)
-
-
VUS
g.167138227G>T
g.166281717G>T
-
-
SCN9A_000216
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/.
1
13
c.2052A>G
r.(?)
p.(Ile684Met)
L1
-
pathogenic
g.167138208T>C
g.166281698T>C
-
-
SCN9A_000035
-
PubMed: Singh 2009
-
-
Germline
-
-
-
-
-
Christoph Lossin
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