Scn2a MGI Mouse Gene Detail - MGI:98248 - sodium channel, voltage-gated, type II, alpha

Symbol

Scn2a
Name

sodium channel, voltage-gated, type II, alpha
Synonyms

A230052E19Rik, Nav1.2, Scn2a1

Feature Type

protein coding gene
IDs

MGI:98248
NCBI Gene: 110876
Gene Overview

MyGene.info: SCN2A
Alliance

gene page
Transcription Start Sites

7 TSS

Sequence Map

Chr2:65620771-65767447 bp, + strand
From Ensembl annotation of GRCm38

View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 38.61 cM
Mapping Data

11 experiments
Sequence Tag

D2Kyo1

SNPs within 2kb

990 from dbSNP Build 142
Strain Annotations

18
PCR

1
RFLP

2

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_98248	protein coding gene	Chr2:65620740-65767448 (.)
129S1/SvImJ	MGP_129S1SvImJ_G0025780	protein coding gene	Chr2:65436785-65575371 (+)
A/J	MGP_AJ_G0025756	protein coding gene	Chr2:62916491-63056916 (+)
AKR/J	MGP_AKRJ_G0025726	protein coding gene	Chr2:64600582-64754626 (+)
BALB/cJ	MGP_BALBcJ_G0025751	protein coding gene	Chr2:63070990-63216774 (+)
C3H/HeJ	MGP_C3HHeJ_G0025512	protein coding gene	Chr2:64791965-64934121 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0026198	protein coding gene	Chr2:67369520-67522890 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0023602	protein coding gene	Chr2:60272107-60401806 (+)
CAST/EiJ	MGP_CASTEiJ_G0024976	protein coding gene	Chr2:64822515-64963371 (+)
CBA/J	MGP_CBAJ_G0025492	protein coding gene	Chr2:69904070-70052332 (+)
DBA/2J	MGP_DBA2J_G0025623	protein coding gene	Chr2:62540223-62681985 (+)
FVB/NJ	MGP_FVBNJ_G0025585	protein coding gene	Chr2:61969423-62110014 (+)
LP/J	MGP_LPJ_G0025711	protein coding gene	Chr2:65261809-65410475 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0025616	protein coding gene	Chr2:71856348-72000271 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0026255	protein coding gene	Chr2:64660210-64807332 (+)
PWK/PhJ	MGP_PWKPhJ_G0024717	protein coding gene	Chr2:62360092-62497669 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0024524	protein coding gene	Chr2:64823443-64971500 (+)
WSB/EiJ	MGP_WSBEiJ_G0025044	protein coding gene	Chr2:65040311-65176971 (+)

Human Ortholog

SCN2A, sodium voltage-gated channel alpha subunit 2

Vertebrate Orthologs

10

Human Ortholog

SCN2A, sodium voltage-gated channel alpha subunit 2
Orthology source: HomoloGene, HGNC
Synonyms

BFIC3, BFIS3, BFNIS, EIEE11, HBA, HBSCI, HBSCII, NAC2, Na(v)1.2, Nav1.2, SCN2A1, SCN2A2
Links

HGNC:10588

NCBI Gene ID: 6326

neXtProt AC: NX_Q99250

UniProt: Q99250
Chr Location

2q24.3; chr2:165208056-165392310 (+) GRCh38.p7

HomoloGene

Vertebrate Homology Class 75001
1 human;1 mouse;1 rat;1 chimpanzee;1 cattle;1 dog;1 chicken;1 zebrafish;1 frog, western clawed;1 macaque, rhesus
HCOP

human homology predictions: SCN2A
Gene Tree

Scn2a

Diseases

1 with human SCN2A associations

				Human Disease	Mouse Models
				benign familial infantile epilepsy IDs benign familial infantile epilepsy DOID:0060169 OMIM:601764 OMIM:605751 OMIM:607745 OMIM:612627 ORDO:306

Click on a disease name to see all genes associated with that disease.

Mutations/Alleles

1 with disease annotations

References

2 with disease annotations

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Phenotype Summary

9 phenotypes from 1 allele in 1 genetic background
7 phenotypes from multigenic genotypes
19 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	immune system	integument	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	neoplasm	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	vision/eye

Click cells to view annotations.

All Mutations and Alleles

6
Chemically induced (other)

1
Gene trapped

1
Targeted

3
Transgenic

1
Genomic Mutations

1 involving Scn2a
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

7 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygotes for a targeted mutation exhibit excess neuronal apoptosis (especially in the brainstem), reduced neuronal sodium channel currents in vitro, and severe hypoxia resulting in neonatal lethality.

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All GO Annotations

41
GO References

10

External Resources

FuncBase

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell death	cell differentiation	cell proliferation	cellular component organization	establishment of localization	homeostatic process	immune system process	lipid metabolic process	nucleic acid-templated transcription	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	non-membrane-bounded organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

35
Tissues

10
cDNA Data

8
Literature Summary

6

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase scn2a

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Scn2a interacts with 440 markers (Mir1a-1, Mir1a-2, Mir1b, ...) View All

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All Sequences

72
RefSeq

10
UniProt

12
CCDS

CCDS38130.1, CCDS84529.1

Ensembl

ENSMUSG00000075318 (Evidence)
NCBI Gene

110876

			Length	Strain/Species	Flank
genomic	ENSMUSG00000075318	Ensembl Gene Model \| MGI Sequence Detail	146677	C57BL/6J	± kb
transcript	ENSMUST00000028377	Ensembl \| MGI Sequence Detail	8935	Not Applicable
polypeptide	ENSMUSP00000028377	Ensembl \| MGI Sequence Detail	2006	Not Applicable

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UniProt

12 Sequences
InterPro Domains

IPR005821 Ion transport domain

IPR000048 IQ motif, EF-hand binding site

IPR010526 Sodium ion transport-associated

IPR027359 Voltage-dependent channel domain superfamily

IPR024583 Voltage-gated Na+ ion channel, cytoplasmic domain

IPR028325 Voltage-gated potassium channel

IPR001696 Voltage gated sodium channel, alpha subunit

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All nucleic 18

cDNA 11

Primer pair 7

Microarray probesets 18

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MGD-MRK-14321, MGI:2444703

Summaries

All 66

Developmental Gene Expression 6

Diseases 2

Gene Ontology 10

Phenotypes 19
Earliest

J:10031 Litt M, et al., Localization of a human brain sodium channel gene (SCN2A) to chromosome 2. Genomics. 1989 Aug;5(2):204-8
Latest

J:265777 Katz E, et al., Role of sodium channel subtype in action potential generation by neocortical pyramidal neurons. Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):E7184-E7192

TSS for Scn2a:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr17985	Chr2:65620757-65620826 (+)	21 bp
Tssr17986	Chr2:65620829-65620834 (+)	61 bp
Tssr17987	Chr2:65620934-65620945 (+)	169 bp
Tssr17988	Chr2:65620962-65620974 (+)	197 bp
Tssr17989	Chr2:65668730-65668746 (+)	47,967 bp
Tssr17990	Chr2:65668753-65668769 (+)	47,990 bp
Tssr17991	Chr2:65765282-65765289 (+)	144,515 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
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