Global Variome shared LOVD
SMN1 (survival of motor neuron 1, telomeric)
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Curator:
Johan den Dunnen
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Unique variants in the SMN1 gene
This database is one of the gene variant databases from the
Leiden Muscular Dystrophy pages
The variants shown are described using the NM_000344.3 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
Classification method
: The method used for the clinical classification of this variant.
All options:
ACMG
ACGS
EAHAD-CFDB
ENIGMA
IARC
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, 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.
86 entries on 1 page. Showing entries 1 - 86.
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Legend
How to query
Effect
Reported
Exon
DNA change (cDNA)
RNA change
Protein
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
+/.
17
_1_9, _1_9_
c.-163_*577{0}
r.0
p.0
ACMG
pathogenic, pathogenic (recessive)
g.(?_70220768)_(70248839_?)del
g.(?_70924941)_(70953012_?)del
del SMN1, NM_000344.3: SMN1 0 copies, NM_000344.3:SMN1 0 copies NM_017411.3:SMN2 3 copies
-
SMN1_000087
ACMG PVS1, PP4_mod
PubMed: Cerino 2022
,
PubMed: Sharifi 2021
-
-
Germline
-
10/432 families SMA, 143/432 families SMA, 15/432 families SMA, 2/432 families SMA, 3/432 families SMA,
4 more items
-
-
-
Johan den Dunnen
+/+
72
_1_9_
c.(?_-163)_(*575_?)del
r.0
p.0
-
pathogenic
g.(?_70220768)_(70248837_?)del
-
1 copy SMN1
-
SMN1_000036
1 copy SMN2, 2 copies SMN2 gene, 3 copies SMN2, 3 copies SMN2 gene, SMN2 1 copy, SMN2 2 copies
Clermont 1997,
PubMed: Martin 2002
,
PubMed: Parsons 1996
,
PubMed: Wirth 2000
,
PubMed: Bai 2014
,
26 more items
-
-
Germline, Unknown
yes
-
-
-
-
Johan den Dunnen
,
Rosário dos Santos
,
Hisahide Nishio
+/.
2
1
c.-14C>T
r.(?)
p.(=)
-
pathogenic
g.70220917C>T
g.70925090C>T
-
-
SMN1_000038
-
PubMed: Parsons 1998
,
OMIM:var0006
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
1
c.-7_9del
r.-7_9del
p.0
-
pathogenic
g.70220924_70220939del
g.70925097_70925112del
-
-
SMN1_000059
-
-
-
-
Germline
-
-
-
-
-
Fang Song
+/.
1
7i_9_
c.(834+1_835-1)_*577{0}
r.?
p.?
-
pathogenic (recessive)
g.(70242004_70247767)_(70248839_?)del
g.(70946177_70951940)_(70953012_?)del
del ex7-8
-
SMN1_000092
-
PubMed: Bai 2022
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
3
_1_9_
c.-163_*577{0}
r.0
p.0
-
pathogenic (recessive)
g.(?_70220768)_(70248839_?)del
g.(?_70924941)_(70953012_?)del
del SMN1
-
SMN1_000087
-
PubMed: Sharifi 2021
-
-
Germline
-
19/432 families SMA, 5/432 families SMA, 7/432 families SMA
-
-
-
Johan den Dunnen
+/.
2
-
c.?
r.?
p.?
-
pathogenic (recessive)
g.?
-
del ex7
-
RAD50_000000
-
PubMed: Reiner 2022
-
-
Germline
-
2/73,755 controls
-
-
-
Johan den Dunnen
+/., ?/.
3
1
c.5C>G
r.(?), r.5c>g
p.(Ala2Gly), p.Ala2Gly
-
pathogenic, VUS
g.70220935C>G
g.70925108C>G
38C>G
-
SMN1_000001
founder mutation likely, normal level SMN1 RNA
PubMed: Bai 2014
,
PubMed: Parsons 1998
,
OMIM:var0006
-
-
Germline
yes
-
-
-
-
Johan den Dunnen
+/.
2
1
c.5C>T
r.5c>u
p.Ala2Val
-
pathogenic
g.70220935C>T
g.70925108C>T
-
-
SMN1_000053
-
PubMed: Yamamoto 2013
-
-
Germline, Unknown
yes
-
-
-
-
Hisahide Nishio
+/.
5
1
c.22dup
r.(?), r.22dup
p.(Ser8Lysfs*23), p.Ser8Lysfs*23
-
pathogenic
g.70220952dup
g.70925125dup
22_23insA
-
SMN1_000002
significantly reduced level SMN1 RNA
PubMed: Bai 2014
,
PubMed: Tsai 2001
-
-
Germline
yes
-
-
-
-
Johan den Dunnen
+/.
1
1
c.40G>T
r.40g>u
p.Glu14*
-
pathogenic
g.70220970G>T
g.70925143G>T
-
-
SMN1_000051
not found in 300 control chromosomes
PubMed: Bai 2014
-
-
Germline
yes
-
-
-
-
Johan den Dunnen
+/.
2
1
c.43C>T
r.(?), r.43c>u
p.(Gln15*), p.Gln15*
-
pathogenic
g.70220973C>T
g.70925146C>T
78C>T
-
SMN1_000003
significantly reduced level SMN1 RNA
PubMed: Bai 2014
,
PubMed: Wirth 1999
-
-
Germline
yes
-
-
-
-
Johan den Dunnen
+/.
1
1
c.48_55dup
r.48_55dup
p.Val19Glyfs*24
-
pathogenic
g.70220978_70220985dup
g.70925151_70925158dup
48_55dupGGATTCCG
-
SMN1_000068
-
PubMed: Kirwin 2013
-
-
Germline
yes
-
-
-
-
Johan den Dunnen
+/.
1
1
c.56del
r.56del
p.Val19Glyfs*21
-
pathogenic
g.70220986del
g.70925159del
-
-
SMN1_000052
significantly reduced level SMN1 RNA
PubMed: Bai 2014
-
-
Germline
yes
-
-
-
-
Johan den Dunnen
+/.
1
1i
c.81+1dupG
r.spl?
p.(?)
-
pathogenic
g.70221012dupG
g.70925185dupG
Q27insG
-
SMN1_000004
-
PubMed: Skordis 2001
-
-
Germline
-
-
-
-
-
Johan den Dunnen
?/.
1
-
c.84C>T
r.(?)
p.(Ser28=)
-
VUS
g.70234668C>T
g.70938841C>T
SMN1(NM_000344.3):c.84C>T (p.S28=)
-
SMN1_000072
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
+/.
1
2
c.88G>A
r.(?)
p.(Asp30Asn)
-
pathogenic
g.70234672G>A
g.70938845G>A
-
-
SMN1_000039
-
PubMed: Sun 2005
,
OMIM:var0012
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
2
c.91dup
r.(?)
p.(Ser31Phefs*2)
-
pathogenic
g.70234675dup
g.70938848dup
124insT
-
SMN1_000005
-
PubMed: Wirth 1999
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
2
c.131A>T
r.(?)
p.(Asp44Val)
-
pathogenic
g.70234715A>T
g.70938888A>T
-
-
SMN1_000040
-
PubMed: Sun 2005
,
OMIM:var0013
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
3
c.208_209insGTGT
r.(?)
p.(Pro70Argfs*3)
-
pathogenic
g.70237270_70237271insGTGT
g.70941443_70941444insGTGT
241-242ins4
-
SMN1_000006
-
PubMed: Wirth 1999
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
3
c.274_284del
r.(?)
p.(Trp92Glyfs*22)
-
pathogenic
g.70238185_70238195del
g.70942358_70942368del
g.348_358del
-
SMN1_000085
-
-
-
-
Germline
-
-
-
-
-
Miloš Brkušanin
+/.
2
4
c.275G>C
r.275g>c
p.Trp92Ser
-
pathogenic
g.70238186G>C
g.70942359G>C
-
-
SMN1_000054
-
PubMed: Yamamoto 2013
-
-
Unknown
-
-
-
-
-
Hisahide Nishio
+/.
2
4
c.283G>C
r.(?)
p.(Gly95Arg)
ACMG
pathogenic, pathogenic (recessive)
g.70238194G>C
g.70942367G>C
-
-
SMN1_000041
-
PubMed: Sharifi 2021
,
PubMed: Sun 2005
,
OMIM:var0014
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
4
c.305G>A
r.274_474del
p.Trp92_Glu158del
-
pathogenic
g.70238216G>A
g.70942389G>A
Trp102X
-
SMN1_000007
-
PubMed: Sossi 2001
,
OMIM:var0010
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+?/.
1
4
c.326A>G
r.(?)
p.(Tyr109Cys)
-
likely pathogenic
g.70238237A>G
g.70942410A>G
-
-
SMN1_000060
-
-
-
-
Germline
-
-
-
-
-
Fang Song
+/.
1
4
c.332C>G
r.(?)
p.(Ala111Gly)
-
pathogenic
g.70238243C>G
g.70942416C>G
-
-
SMN1_000042
-
PubMed: Sun 2005
,
OMIM:var0015
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
4
c.346A>T
r.(?)
p.(Ile116Phe)
-
pathogenic
g.70238257A>T
g.70942430A>T
-
-
SMN1_000044
-
PubMed: Cusco 2004
,
OMIM:var0017
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
5
4
c.399_402del
r.(?)
p.(Glu134Serfs*14)
-
pathogenic
g.70238310_70238313del
g.70942483_70942486del
430del4
-
SMN1_000008
-
PubMed: Bussaglia 1995
,
PubMed: Cusco 2003
,
OMIM:var0011
,
PubMed: Martin 2002
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
4
c.400G>A
r.(?)
p.(Glu134Lys)
-
pathogenic
g.70238311G>A
g.70942484G>A
433G>A
-
SMN1_000009
-
Clermont 1997,
PubMed: Wirth 2000
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
4
c.406C>G
r.(?)
p.(Gln136Glu)
-
pathogenic
g.70238317C>G
g.70942490C>G
-
-
SMN1_000045
-
PubMed: Cusco 2004
,
OMIM:var0018
-
-
Germline
-
-
-
-
-
Johan den Dunnen
?/.
1
-
c.421C>T
r.(?)
p.(Leu141=)
-
VUS
g.70238332C>T
g.70942505C>T
SMN1(NM_000344.3):c.421C>T (p.L141=)
-
SMN1_000073
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
+/.
2
4
c.439_443del
r.(?), r.439_443del
p.(Glu147Serfs*2), p.Glu147Serfs*2
-
pathogenic
g.70238350_70238354del
g.70942523_70942527del
425del5, 425del5 and 472del5
-
SMN1_000010
-
PubMed: Brahe 1996
,
PubMed: Sossi 2001
,
OMIM:var0009
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-/.
1
-
c.462A>G
r.(?)
p.(Gln154=)
-
benign
g.70238373A>G
g.70942546A>G
SMN1(NM_000344.3):c.462A>G (p.Q154=)
-
SMN1_000074
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
+?/.
1
5
c.475-2A>T
r.spl
p.?
-
likely pathogenic
g.70238543A>T
g.70942716A>T
-
-
SMN1_000079
-
-
-
-
Germline/De novo (untested)
yes
-
-
-
-
Kyriaki Kekou
+?/.
1
5
c.489_493del
r.(?)
p.(Gln164Phefs*4)
-
likely pathogenic
g.70238559_70238563del
g.70942732_70942736del
489_493delCCAAG
-
SMN1_000076
-
-
-
-
De novo
?
-
-
-
-
Kyriaki Kekou
+/.
1
5
c.510_511del
r.(?)
p.(fs*)
-
pathogenic
g.70238580_70238581del
g.70942753_70942754del
542delGT
-
SMN1_000011
-
PubMed: Parsons 1998
,
PubMed: Parsons 1998
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
5
c.524del
r.(?)
p.(Ser175Phefs*38)
-
pathogenic
g.70238594del
g.70942767del
-
-
SMN1_000046
-
-
-
-
Germline
-
-
-
-
-
Rosário dos Santos
+/.
1
-
c.536_540del
r.(?)
p.(Lys179Argfs*2)
-
pathogenic
g.70238606_70238610del
g.70942779_70942783del
-
-
SMN1_000083
localisation of fs-mutation (in SMN1 or SMN2) not analysed yet
-
-
-
Germline/De novo (untested)
-
-
-
-
-
Gemeinschaftspraxis für Humangenetik Dresden
+/.
1
-
c.542A>G
r.(?)
p.(Asp181Gly)
-
pathogenic
g.70238612A>G
g.70942785A>G
SMN1(NM_000344.3):c.542A>G (p.D181G)
-
SMN1_000075
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
+/., +?/.
2
-
c.549del
r.(?)
p.(Lys184Serfs*29)
ACMG
likely pathogenic (recessive), pathogenic (recessive)
g.70238619del
g.70942792del
c.549delC
-
SMN1_000088
ACMG: PVS1, PM2_SUP
PubMed: Sharifi 2021
VCV001699219.1
-
Germline
yes
-
-
-
-
Johan den Dunnen
,
Andreas Laner
+?/.
1
5
c.551dup
r.(551dup)
p.(Pro185Alafs*71)
-
likely pathogenic
g.70238621dup
g.70942794dup
-
-
SMN1_000080
-
-
-
-
Germline
-
-
-
-
-
Kyriaki Kekou
+/.
1
5
c.558del
r.(?)
p.(Lys186Asnfs*27)
-
pathogenic
g.70238628del
g.70942801del
591delA
-
SMN1_000012
-
PubMed: Wirth 1999
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
5
c.585dup
r.(?)
p.(Pro196Serfs*60)
-
pathogenic
g.70238655dup
g.70942828dup
618insT
-
SMN1_000013
-
Clermont 1997,
PubMed: Wirth 2000
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
5i_7i
c.628-?_834+?del
r.(?)
p.(?)
-
pathogenic
g.70240485_70242003del
g.70944658_70946176del
IVS4_IVS6del
-
SMN1_000014
1 more item
PubMed: Wirth 1999
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+?/.
1
7
c.637_658del
r.(637_658del)
p.(Lys213Hisfs*23)
-
likely pathogenic
g.70240494_70240515del
g.70944667_70944688del
-
-
SMN1_000077
-
-
-
-
Germline/De novo (untested)
-
-
-
-
-
Kyriaki Kekou
?/.
1
6
c.662C>T
r.662c>u
p.Pro221Leu
-
VUS
g.70240519C>T
g.70944692C>T
-
-
SMN1_000069
-
PubMed: Kirwin 2013
-
-
Germline
yes
-
-
-
-
Johan den Dunnen
+/.
2
5, 6
c.683T>A
r.(?), r.683u>a
p.(Leu228*), p.Leu228*
-
pathogenic
g.70240540T>A
g.70944713T>A
-
-
SMN1_000015
significantly reduced level SMN1 RNA
PubMed: Bai 2014
,
PubMed: Tsai 2001
-
-
Germline
yes
-
-
-
-
Johan den Dunnen
+?/.
2
5
c.689C>T
r.689c>u
p.Ser230Leu
-
likely pathogenic
g.70240546C>T
g.70944719C>T
-
-
SMN1_000058
-
-
-
-
Germline
-
-
-
-
-
Fang Song
+/.
2
7i_9i
c.(723+1_724-1)_(*3+1_*4-1)del
r.(del), r.?
p.?
-
pathogenic, pathogenic (recessive)
g.(70240581_70241892)_(70247822_70248265)del
9.(70944754_70946065)_(70951995_70952438)del
del ex7-8
-
SMN1_000050
-
PubMed: Bell 2011
,
PubMed: Xia 2021
-
-
Germline
-
-
-
-
-
Gerard C.P. Schaafsma
,
Johan den Dunnen
+/.
1
7
c.734C>T
r.(?)
p.(Pro245Leu)
-
pathogenic
g.70241903C>T
g.70946076C>T
767C>T
-
SMN1_000016
-
PubMed: Rochette 1997
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
7
c.734dup
r.734dup
p.Pro246Thrfs*10
-
pathogenic
g.70241903dup
g.70946076dup
-
-
SMN1_000037
-
-
-
-
Germline
-
-
-
-
-
Rosário dos Santos
+/.
1
-
c.735dup
r.(?)
p.(Pro246ThrfsTer10)
ACMG
pathogenic (recessive)
g.70241904dup
g.70946077dup
c.735_736insA
-
SMN1_000089
-
PubMed: Sharifi 2021
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
7
c.740dup
r.(?)
p.(Pro248Serfs*8)
-
pathogenic
g.70241909dup
g.70946082dup
773insC
-
SMN1_000017
-
PubMed: Martin 2002
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+?/.
1
7
c.744del
r.(?)
p.(Ile249Tyrfs*16)
-
likely pathogenic
g.70241913del
g.70946086del
(Pro247Profs*17)
-
SMN1_000064
-
-
-
-
Germline
-
-
-
-
-
Fang Song
?/.
1
7
c.767A>T
r.spl?
p.(Asp256Val)
-
VUS
g.70241936A>T
g.70946109A>T
-
-
SMN1_000078
-
-
-
-
Germline/De novo (untested)
-
-
-
-
-
Kyriaki Kekou
+/.
5
7
c.770_780dup
r.(?), r.770_780dup
p.(Gly261Leufs*8), p.Gly261Leufs*8
-
pathogenic
g.70241939_70241949dup
g.70946112_70946122dup
813ins/dup11 and 800ins11
-
SMN1_000018
-
Clermont 1997,
PubMed: Martin 2002
,
PubMed: Parsons 1996
,
PubMed: Wirth 2000
,
1 more item
-
-
Germline
-
-
-
-
-
Johan den Dunnen
,
Rosário dos Santos
+/.
1
7
c.784A>G
r.(?)
p.(Ser262Gly)
-
pathogenic
g.70241953A>G
g.70946126A>G
-
-
SMN1_000043
-
PubMed: Sun 2005
,
OMIM:var0016
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
7
c.785G>T
r.(?)
p.(Ser262Ile)
-
pathogenic
g.70241954G>T
g.70946127G>T
818G>T
-
SMN1_000019
-
PubMed: Hahnen 1997
,
OMIM:var0003
,
PubMed: McAndrew 1997
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+?/.
1
7
c.811_814dup
r.(?)
p.(Tyr272Trpfs*35)
-
likely pathogenic
g.70241980_70241983dup
g.70946153_70946156dup
-
-
SMN1_000062
-
-
-
-
Germline
-
-
-
-
-
Fang Song
+/., +?/.
3
7
c.815A>G
r.(?)
p.(Tyr272Cys)
ACMG
likely pathogenic (recessive), pathogenic
g.70241984A>G
g.70946157A>G
848A>G
-
SMN1_000021
ACMG: PS4, PM3, PS3_SUP, PM2_SUP, PP3
PubMed: Lefebvre 1995
,
OMIM:var0004
,
PubMed: Rochette 1997
,
PubMed: Wirth 2000
,
PubMed: Wirth 1999
VCV000009166.3
-
Germline
yes
-
-
-
-
Johan den Dunnen
,
Andreas Laner
+/.
1
7
c.819dup
r.819dup
p.Thr274Tyrfs*32
-
pathogenic
g.70241988dup
g.70946161dup
819_820insT
-
SMN1_000055
-
PubMed: Yamamoto 2013
-
-
Unknown
-
-
-
-
-
Hisahide Nishio
+/.
3
7
c.821C>T
r.(?)
p.(Thr274Ile)
-
pathogenic
g.70241990C>T
g.70946163C>T
854C>T
-
SMN1_000022
haplotype shared with other German family
PubMed: Hahnen 1997
,
OMIM:var0002
,
1 more item
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
7
c.823G>A
r.(?)
p.(Gly275Ser)
-
pathogenic
g.70241992G>A
g.70946165G>A
-
-
SMN1_000023
-
PubMed: Skordis 2001
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
7
c.830A>G
r.830a>g
p.Tyr277Cys
-
pathogenic
g.70241999A>G
g.70946172A>G
-
-
SMN1_000056
-
PubMed: Yamamoto 2013
-
-
Unknown
-
-
-
-
-
Hisahide Nishio
+/.
1
7i
c.834+2T>G
r.spl?
p.(?)
-
pathogenic
g.70242005T>G
g.70946178T>G
867+2T>G
-
SMN1_000024
-
PubMed: Martin 2002
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-/.
1
7i
c.835-24dup
r.(=)
p.(=)
-
benign
g.70247744dup
g.70951917dup
-
-
SMN1_000035
-
PubMed: Ogino 2002
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
6i
c.835-23_835-22insNC_000004.11:81302538_81302865{81302854C>A}
r.spl
p.?
-
pathogenic
g.?
-
hg19 chr5:g.70247745_70247746insNC_000004.11:81302538_81302865{81302854C>A}
-
SMN1_000067
insertion occurs in intron 6 branch point, predicted to alter splicing of exon 7
-
-
-
Germline
yes
-
-
-
-
Kathleen Vinette
+/.
1
7i
c.835-18_835-12del
r.(spl?)
p.(?)
-
pathogenic
g.70247750_70247756del
g.70951923_70951929del
868-11del7
-
SMN1_000025
-
PubMed: Lefebvre 1995
,
PubMed: Wirth 2000
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
7i
c.835-5T>G
r.835_*3del
p.Gly279Glufs*5
-
pathogenic
g.70247763T>G
g.70951936T>G
-
-
SMN1_000063
-
-
-
-
Germline
-
-
-
-
-
Fang Song
?/.
1
7i
c.835-3C>T
r.(?)
p.(=)
-
VUS
g.70247765C>T
g.70951938C>T
-
-
SMN1_000049
-
-
-
-
Germline
-
-
-
-
-
Pascale Saugier-Veber
+/.
1
6i_8i
c.(724+1_835-1)_(*3+1_*4-1)del
r.?
p.?
-
pathogenic (recessive)
g.(70241894_70247767)_(70247822_70248265)del
-
1 copy ex7-8 SMN1
-
SMN1_000084
-
-
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
7i_8i
c.(834+1_835-1)_(*3+1_*4-1)del
r.?
p.?
-
pathogenic (recessive)
g.(70242004_70247767)_(70247822_70248265)del
g.(70946177_70951940)_(70951995_70952438)del
del ex7
-
SMN1_000086
-
PubMed: Sharifi 2021
-
-
Germline
-
7/432 families SMA
-
-
-
Johan den Dunnen
+/.
4
7i_8i, _7i_8i_
c.(?_835-1)_(*3+1_?)del
r.?, r.spl?
p.?
-
pathogenic, pathogenic (recessive)
g.(?_70247767)_(70247822_?)del
-
0 SMN1, ex7 del homozygous)
-
SMN1_000082
-
PubMed: Prior 2009
-
-
Germline
-
-
-
-
-
Johan den Dunnen
,
Sha Hong
+/.
1
-
c.835G>C
r.(?)
p.(Gly279Arg)
-
pathogenic (recessive)
g.70247768G>C
-
-
-
SMN1_000091
-
PubMed: Bai 2022
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
8
c.835G>T
r.(?), r.(spl?)
p.(Gly279Cys)
ACMG
pathogenic, pathogenic (recessive)
g.70247768G>T
g.70951941G>T
868G>T
-
SMN1_000026
-
PubMed: Sharifi 2021
,
PubMed: Wang 1998
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
8
c.836G>T
r.(?)
p.(Gly279Val)
-
pathogenic
g.70247769G>T
g.70951942G>T
869G>T
-
SMN1_000027
-
PubMed: Talbot 1997
,
OMIM:var0005
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+?/.
1
-
c.838T>A
r.(?)
p.(Phe280Ile)
ACMG
likely pathogenic (recessive)
g.70247771T>A
g.70951944T>A
-
-
SMN1_000090
-
PubMed: Sharifi 2021
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/., -/., ?/.
3
8
c.(840C>T), c.840C>T
r.(?), r.spl, r.spl?
p.(=), p.(Phe280=), p.?
-
benign, pathogenic (recessive), VUS
g.70247773C>T
g.70951946C>T
SMN1(NM_000344.3):c.840C>T (p.F280=)
-
SMN1_000047
difference with SMN2 gene, VKGL data sharing initiative Nederland
PubMed: Sharifi 2021
-
-
CLASSIFICATION record, Germline
-
3/432 families SMA
-
-
-
Johan den Dunnen
,
VKGL-NL_Utrecht
+?/.
3
8
c.863G>T
r.835_*3del
p.Gly279Glufs*5
-
likely pathogenic
g.70247796G>T
g.70951969G>T
-
-
SMN1_000057
-
-
-
-
Germline
-
-
-
-
-
Fang Song
+/.
2
8i
c.*3+4_*3+7del
r.spl?
p.(?)
-
pathogenic
g.70247825_70247828del
g.70951998_70952001del
922+3del4
-
SMN1_000028
-
PubMed: Lefebvre 1995
,
PubMed: Wirth 2000
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
8i
c.*3+6T>G
r.(spl?)
p.(?)
-
pathogenic
g.70247827T>G
g.70952000T>G
922+6T>G
-
SMN1_000029
-
PubMed: Lorson 1999
,
OMIM:var0008
,
PubMed: Wirth 1999
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-?/.
1
8i
c.*3+80T>G
r.(?)
p.(=)
-
likely benign
g.70247901T>G
g.70952074T>G
g.27134T>G
-
SMN1_000070
-
-
-
rs143838139
Germline
-
-
-
-
-
Laura Alías
+/.
3
8i
c.(*3+1_*4-1)_(*575_?)del
r.(?)
p.(?)
-
pathogenic
g.(70247822_70248265)_(70248837_?)del
-
del exon 8
-
SMN1_000030
-
PubMed: Gambardella 1998
,
OMIM:var0007
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-?/.
4
10, 9
c.*211_*212del
r.(=), r.(?)
p.(=)
-
likely benign
g.70248473_70248474del
g.70952646_70952647del, g.70952647_70952648del
*210_*211del, *210_*211del g.27706_27707delAT, SMN1(NM_000344.4):c.*211_*212delAT
-
SMN1_000071
VKGL data sharing initiative Nederland,
1 more item
-
-
rs200800214
CLASSIFICATION record, Germline
-
-
-
-
-
VKGL-NL_AMC
,
Laura Alías
?/.
1
9
c.(*239G>A)
r.(?)
p.(=)
-
VUS
g.70248501G>A
g.70952674G>A
-
-
SMN1_000048
difference with SMN2 gene
-
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-/.
1
9
c.*338_*339delinsGC
r.(?)
p.(=)
-
benign
g.70248600_70248601delinsGC
g.70952773_70952774delinsGC
-
-
SMN1_000032
-
-
-
-
Germline
-
-
-
-
-
Johan den Dunnen
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