SCNM1 (sodium channel modifier 1) - Rat Genome Database

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Gene: SCNM1 (sodium channel modifier 1) Homo sapiens
Analyze
Symbol: SCNM1
Name: sodium channel modifier 1
RGD ID: 36174167
HGNC Page HGNC:23136
Description: Enables enzyme binding activity. Predicted to be involved in alternative mRNA splicing, via spliceosome. Predicted to be located in nuclear speck. Predicted to be part of spliceosomal complex. Predicted to be active in nucleus. Implicated in orofaciodigital syndrome XIX.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: OFD19
RGD Orthologs
Mouse
Dog
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381151,166,144 - 151,170,296 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1151,156,664 - 151,170,296 (+)EnsemblGRCh38hg38GRCh38
GRCh371151,138,620 - 151,142,772 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map1q21.3NCBI
HuRef1122,516,524 - 122,520,863 (+)NCBIHuRef
CHM1_11152,533,825 - 152,538,100 (+)NCBICHM1_1
T2T-CHM13v2.01150,289,872 - 150,294,025 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nuclear speck  (IEA,ISS)
nucleoplasm  (IEA)
nucleus  (IBA,IEA)
spliceosomal complex  (IEA)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:7566098   PMID:12477932   PMID:12920299   PMID:14702039   PMID:15489334   PMID:16189514   PMID:16710414   PMID:17656373   PMID:18482256   PMID:21873635   PMID:22810586   PMID:23382074  
PMID:24705354   PMID:25416956   PMID:26186194   PMID:26496610   PMID:27107012   PMID:28514442   PMID:29892012   PMID:31515488   PMID:32296183   PMID:32814053   PMID:33742100   PMID:33961781  
PMID:35271311   PMID:35944360   PMID:36084634   PMID:36949045   PMID:36966392   PMID:38360978  


Genomics

Comparative Map Data
SCNM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381151,166,144 - 151,170,296 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1151,156,664 - 151,170,296 (+)EnsemblGRCh38hg38GRCh38
GRCh371151,138,620 - 151,142,772 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map1q21.3NCBI
HuRef1122,516,524 - 122,520,863 (+)NCBIHuRef
CHM1_11152,533,825 - 152,538,100 (+)NCBICHM1_1
T2T-CHM13v2.01150,289,872 - 150,294,025 (+)NCBIT2T-CHM13v2.0
Scnm1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39395,037,030 - 95,041,285 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl395,036,847 - 95,041,322 (-)EnsemblGRCm39 Ensembl
GRCm38395,129,719 - 95,134,050 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl395,129,536 - 95,134,011 (-)EnsemblGRCm38mm10GRCm38
MGSCv37394,933,641 - 94,937,934 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36395,215,123 - 95,219,392 (-)NCBIMGSCv36mm8
Celera396,560,854 - 96,565,147 (-)NCBICelera
Cytogenetic Map3F2.1NCBI
cM Map340.74NCBI
SCNM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11760,231,034 - 60,233,349 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1760,231,104 - 60,233,337 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1759,674,590 - 59,676,909 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01761,247,120 - 61,249,439 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1761,247,195 - 61,249,427 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11760,075,855 - 60,078,174 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01760,161,177 - 60,163,496 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01760,888,949 - 60,891,269 (+)NCBIUU_Cfam_GSD_1.0

Variants

.
Variants in SCNM1
18 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_024041.4(SCNM1):c.590G>A (p.Arg197Gln) single nucleotide variant not specified [RCV004318100] Chr1:151168335 [GRCh38]
Chr1:151140811 [GRCh37]
Chr1:1q21.3		 uncertain significance
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684) copy number gain See cases [RCV000510926] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh38/hg38 1q21.3(chr1:150989333-151584777)x1 copy number loss See cases [RCV000138949] Chr1:150989333..151584777 [GRCh38]
Chr1:150961809..151557253 [GRCh37]
Chr1:149228433..149823877 [NCBI36]
Chr1:1q21.3		 likely pathogenic
GRCh37/hg19 1p36.33-q44(chr1:47851-249228449)x3 copy number gain not provided [RCV000736295] Chr1:47851..249228449 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:82154-249218992)x3 copy number gain not provided [RCV000736305] Chr1:82154..249218992 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh38/hg38 1q21.2-25.2(chr1:149854269-180267197)x3 copy number gain See cases [RCV000143515] Chr1:149854269..180267197 [GRCh38]
Chr1:149825831..180236332 [GRCh37]
Chr1:148092455..178502955 [NCBI36]
Chr1:1q21.2-25.2		 pathogenic
GRCh37/hg19 1q21.1-21.3(chr1:143753740-151399970)x3 copy number gain See cases [RCV000447109] Chr1:143753740..151399970 [GRCh37]
Chr1:1q21.1-21.3		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3 copy number gain See cases [RCV000510383] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1q21.3(chr1:150853044-154647786)x3 copy number gain not provided [RCV000684655] Chr1:150853044..154647786 [GRCh37]
Chr1:1q21.3		 pathogenic
GRCh37/hg19 1q21.1-21.3(chr1:144927578-153223600)x3 copy number gain Chromosome 1q21.1 duplication syndrome [RCV000223957] Chr1:144927578..153223600 [GRCh37]
Chr1:1q21.1-21.3		 pathogenic
NC_000001.10:g.(?_130980840)_(248900000_?)dup duplication Gastrointestinal stromal tumor [RCV001300221]|Parathyroid carcinoma [RCV001341077] Chr1:130980840..248900000 [GRCh37]
Chr1:1q12-44		 uncertain significance
NC_000001.10:g.(?_151122490)_(151585008_?)dup duplication Severe myoclonic epilepsy in infancy [RCV001324071] Chr1:151122490..151585008 [GRCh37]
Chr1:1q21.3		 uncertain significance
NC_000001.10:g.(?_149895434)_(156851434_?)dup duplication Autosomal recessive mendelian susceptibility to mycobacterial diseases due to complete RORgamma receptor deficiency [RCV001958273]|Congenital neutropenia-myelofibrosis-nephromegaly syndrome [RCV001958271]|Kostmann syndrome [RCV003120769]|MHC class II deficiency [RCV001992607] Chr1:149895434..156851434 [GRCh37]
Chr1:1q21.2-23.1		 uncertain significance
NM_024041.4(SCNM1):c.187del (p.Arg63fs) deletion Orofaciodigital syndrome 19 [RCV002294747] Chr1:151166997 [GRCh38]
Chr1:151139473 [GRCh37]
Chr1:1q21.3		 pathogenic
NM_024041.4:c.301_302ins[N[324];285_301] insertion Orofaciodigital syndrome 19 [RCV002294746]   pathogenic
NM_024041.4(SCNM1):c.152C>A (p.Pro51Gln) single nucleotide variant Orofaciodigital syndrome 19 [RCV002294745] Chr1:151166963 [GRCh38]
Chr1:151139439 [GRCh37]
Chr1:1q21.3		 pathogenic
NM_024041.4(SCNM1):c.59G>A (p.Arg20Lys) single nucleotide variant not specified [RCV004313983] Chr1:151166478 [GRCh38]
Chr1:151138954 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_024041.4(SCNM1):c.9C>G (p.Phe3Leu) single nucleotide variant not specified [RCV004090281] Chr1:151166161 [GRCh38]
Chr1:151138637 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_024041.4(SCNM1):c.140G>T (p.Cys47Phe) single nucleotide variant not specified [RCV004153244] Chr1:151166951 [GRCh38]
Chr1:151139427 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_024041.4(SCNM1):c.627G>C (p.Trp209Cys) single nucleotide variant not specified [RCV004121589] Chr1:151169019 [GRCh38]
Chr1:151141495 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_024041.4(SCNM1):c.5C>G (p.Ser2Cys) single nucleotide variant not specified [RCV004117728] Chr1:151166157 [GRCh38]
Chr1:151138633 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_024041.4(SCNM1):c.365C>G (p.Pro122Arg) single nucleotide variant not specified [RCV004171216] Chr1:151167381 [GRCh38]
Chr1:151139857 [GRCh37]
Chr1:1q21.3		 uncertain significance
GRCh37/hg19 1q12-23.1(chr1:142535935-157648813)x3 copy number gain Chromosome 1q21.1 duplication syndrome [RCV003329522] Chr1:142535935..157648813 [GRCh37]
Chr1:1q12-23.1		 pathogenic
NM_024041.4(SCNM1):c.421G>A (p.Val141Ile) single nucleotide variant not specified [RCV004340578] Chr1:151168166 [GRCh38]
Chr1:151140642 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_024041.4(SCNM1):c.521C>T (p.Ala174Val) single nucleotide variant not provided [RCV003408863] Chr1:151168266 [GRCh38]
Chr1:151140742 [GRCh37]
Chr1:1q21.3		 likely benign
GRCh37/hg19 1q21.1-23.1(chr1:144368497-158992086)x3 copy number gain not specified [RCV003986717] Chr1:144368497..158992086 [GRCh37]
Chr1:1q21.1-23.1		 pathogenic
GRCh37/hg19 1q21.1-23.1(chr1:146577511-157155587)x3 copy number gain not specified [RCV003987261] Chr1:146577511..157155587 [GRCh37]
Chr1:1q21.1-23.1		 pathogenic
NM_024041.4(SCNM1):c.484C>A (p.Pro162Thr) single nucleotide variant not specified [RCV004454958] Chr1:151168229 [GRCh38]
Chr1:151140705 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_024041.4(SCNM1):c.583A>G (p.Thr195Ala) single nucleotide variant not specified [RCV004454959] Chr1:151168328 [GRCh38]
Chr1:151140804 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_024041.4(SCNM1):c.74T>A (p.Leu25Gln) single nucleotide variant not specified [RCV004454960] Chr1:151166493 [GRCh38]
Chr1:151138969 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_024041.4(SCNM1):c.14G>A (p.Arg5Lys) single nucleotide variant not specified [RCV004454955] Chr1:151166166 [GRCh38]
Chr1:151138642 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_024041.4(SCNM1):c.364C>G (p.Pro122Ala) single nucleotide variant not specified [RCV004454956] Chr1:151167380 [GRCh38]
Chr1:151139856 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_024041.4(SCNM1):c.367C>A (p.His123Asn) single nucleotide variant not specified [RCV004454957] Chr1:151167383 [GRCh38]
Chr1:151139859 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_024041.4(SCNM1):c.580C>T (p.Leu194Phe) single nucleotide variant not specified [RCV004658814] Chr1:151168325 [GRCh38]
Chr1:151140801 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_024041.4(SCNM1):c.338T>C (p.Ile113Thr) single nucleotide variant not specified [RCV004658815] Chr1:151167354 [GRCh38]
Chr1:151139830 [GRCh37]
Chr1:1q21.3		 uncertain significance

QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
406926673GWAS575649_Hbody height QTL GWAS575649 (human)0.0000003body height (VT:0001253)body height (CMO:0000106)1151168737151168738Human
1357381BW57_HBody weight QTL 57 (human)10.0001Body weightfat free mass after exercise training1140630236166630236Human


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENST00000368902   ⟹   ENSP00000357898
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1151,166,079 - 151,169,138 (+)Ensembl
Ensembl Acc Id: ENST00000368905   ⟹   ENSP00000357901
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1151,166,144 - 151,170,296 (+)Ensembl
Ensembl Acc Id: ENST00000459799
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1151,167,868 - 151,169,133 (+)Ensembl
Ensembl Acc Id: ENST00000461862
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1151,166,022 - 151,167,979 (+)Ensembl
Ensembl Acc Id: ENST00000471039
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1151,166,066 - 151,166,950 (+)Ensembl
Ensembl Acc Id: ENST00000497147
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1151,166,669 - 151,169,111 (+)Ensembl
Ensembl Acc Id: ENST00000602841   ⟹   ENSP00000473282
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1151,156,664 - 151,169,133 (+)Ensembl
RefSeq Acc Id: NM_001204856   ⟹   NP_001191785
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381151,166,144 - 151,170,296 (+)NCBI
T2T-CHM13v2.01150,289,872 - 150,294,025 (+)NCBI
Sequence:
RefSeq Acc Id: NM_024041   ⟹   NP_076946
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381151,166,144 - 151,170,296 (+)NCBI
T2T-CHM13v2.01150,289,872 - 150,294,025 (+)NCBI
Sequence:
RefSeq Acc Id: NR_037937
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381151,166,144 - 151,170,296 (+)NCBI
T2T-CHM13v2.01150,289,872 - 150,294,025 (+)NCBI
Sequence:
RefSeq Acc Id: NP_001191785   ⟸   NM_001204856
- Peptide Label: isoform 2
- UniProtKB: Q9BWG6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_076946   ⟸   NM_024041
- Peptide Label: isoform 1
- UniProtKB: B4DWR1 (UniProtKB/Swiss-Prot),   Q5JR74 (UniProtKB/Swiss-Prot),   Q9BWG6 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSP00000473282   ⟸   ENST00000602841
Ensembl Acc Id: ENSP00000357898   ⟸   ENST00000368902
Ensembl Acc Id: ENSP00000357901   ⟸   ENST00000368905

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9BWG6-F1-model_v2 AlphaFold Q9BWG6 1-230 view protein structure


Additional Information

Database Acc Id Source(s)
COSMIC SCNM1 COSMIC
Ensembl Genes ENSG00000163156 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000368902 ENTREZGENE
  ENST00000368902.1 UniProtKB/Swiss-Prot
  ENST00000368905 ENTREZGENE
  ENST00000368905.9 UniProtKB/Swiss-Prot
  ENST00000602841.5 UniProtKB/Swiss-Prot
GTEx ENSG00000163156 GTEx
HGNC ID HGNC:23136 ENTREZGENE
Human Proteome Map SCNM1 Human Proteome Map
InterPro SCNM1 UniProtKB/Swiss-Prot
  SCNM1_acidic UniProtKB/Swiss-Prot
  Znf-SCNM1 UniProtKB/Swiss-Prot
KEGG Report hsa:100534012 UniProtKB/Swiss-Prot
  hsa:79005 UniProtKB/Swiss-Prot
NCBI Gene SCNM1 ENTREZGENE
OMIM 608095 OMIM
PANTHER PTHR32297 UniProtKB/Swiss-Prot
  SODIUM CHANNEL MODIFIER 1 UniProtKB/Swiss-Prot
Pfam SCNM1_acidic UniProtKB/Swiss-Prot
  zf-SCNM1 UniProtKB/Swiss-Prot
PharmGKB PA134958437 PharmGKB
UniProt B4DWR1 ENTREZGENE
  Q5JR74 ENTREZGENE
  Q9BWG6 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary B4DWR1 UniProtKB/Swiss-Prot
  Q5JR74 UniProtKB/Swiss-Prot