Mutagenetix > Incidental Mutation

Incidental Mutation 'R7240:Scn3a'

563126

Institutional Source

Beutler Lab

Gene Symbol

Scn3a

Ensembl Gene

ENSMUSG00000057182

Gene Name

sodium channel, voltage-gated, type III, alpha

Synonyms

Nav1.3, LOC381367

MMRRC Submission

045347-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7240 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

65457118-65567627 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 65469042 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 1373 (D1373E)

Ref Sequence

ENSEMBL: ENSMUSP00000065023 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000066432] [ENSMUST00000100069]

AlphaFold

A2ASI5

Predicted Effect

possibly damaging
Transcript: ENSMUST00000066432
AA Change: D1373E

PolyPhen 2 Score 0.772 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000065023
Gene: ENSMUSG00000057182
AA Change: D1373E

Domain	Start	End	E-Value	Type
low complexity region	23	40	N/A	INTRINSIC
Pfam:Ion_trans	127	435	5.2e-83	PFAM
low complexity region	473	498	N/A	INTRINSIC
Pfam:Na_trans_cytopl	504	626	2e-42	PFAM
Pfam:Ion_trans	710	945	1.4e-58	PFAM
Pfam:Na_trans_assoc	949	1153	2.7e-58	PFAM
Pfam:Ion_trans	1157	1430	3e-67	PFAM
Pfam:Ion_trans	1477	1734	6.3e-55	PFAM
Pfam:PKD_channel	1573	1728	8e-7	PFAM
IQ	1851	1873	5.75e-2	SMART
low complexity region	1913	1921	N/A	INTRINSIC
low complexity region	1927	1943	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000100069
AA Change: D1373E

PolyPhen 2 Score 0.772 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000097647
Gene: ENSMUSG00000057182
AA Change: D1373E

Domain	Start	End	E-Value	Type
low complexity region	23	40	N/A	INTRINSIC
Pfam:Ion_trans	127	435	5.2e-83	PFAM
low complexity region	473	498	N/A	INTRINSIC
Pfam:Na_trans_cytopl	504	626	2e-42	PFAM
Pfam:Ion_trans	710	945	1.4e-58	PFAM
Pfam:Na_trans_assoc	949	1153	2.7e-58	PFAM
Pfam:Ion_trans	1157	1430	3e-67	PFAM
Pfam:Ion_trans	1477	1734	6.3e-55	PFAM
Pfam:PKD_channel	1573	1728	8e-7	PFAM
IQ	1851	1873	5.75e-2	SMART
low complexity region	1913	1921	N/A	INTRINSIC
low complexity region	1927	1943	N/A	INTRINSIC

Meta Mutation Damage Score

0.1654

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

96% (50/52)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with 24 transmembrane domains and one or more regulatory beta subunits. They are responsible for the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel alpha subunit gene family, and is found in a cluster of five alpha subunit genes on chromosome 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutation of this gene results in lethality of most mutants by weaning. Heterozygous mice exhibit improved glucose tolerance. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 51 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2210017I01Rik	A	G	3: 92,605,075 (GRCm38)	I59T	unknown	Het
Aspm	C	T	1: 139,478,651 (GRCm38)	Q1759*	probably null	Het
Atn1	A	T	6: 124,747,898 (GRCm38)	I124K	unknown	Het
Catsper2	TAGGATGGCTTTTCTCAGGATAGCTTTTCTCAGGATGGCTTTTCTCAGGATAGCTTTTCTCAGGATGGCTTTTCTCAGGATAGCTTTTCT	TAGGATGGCTTTTCTCAGGATAGCTTTTCTCAGGATGGCTTTTCTCAGGATAGCTTTTCT	2: 121,397,572 (GRCm38)		probably benign	Het
Ccdc88c	C	T	12: 100,944,939 (GRCm38)	V879M	probably benign	Het
Cd300c	A	G	11: 114,959,783 (GRCm38)	C65R	possibly damaging	Het
Cd69	A	T	6: 129,270,042 (GRCm38)	S112T	possibly damaging	Het
Cdh19	T	C	1: 110,893,407 (GRCm38)	T534A	probably benign	Het
Cdk5rap2	T	A	4: 70,291,908 (GRCm38)	D701V	probably damaging	Het
D130052B06Rik	A	G	11: 33,623,874 (GRCm38)	H157R	possibly damaging	Het
Dpf1	T	A	7: 29,311,627 (GRCm38)	F150L	probably benign	Het
Dsg1c	T	C	18: 20,283,109 (GRCm38)	L689P	probably damaging	Het
Dstyk	G	A	1: 132,454,123 (GRCm38)	M538I	probably benign	Het
E4f1	T	A	17: 24,444,325 (GRCm38)	I669F	probably damaging	Het
Gm7138	T	C	10: 77,776,755 (GRCm38)	T64A	unknown	Het
Gnai2	A	C	9: 107,615,773 (GRCm38)	D310E		Het
Iqca	A	G	1: 90,070,550 (GRCm38)	V567A	possibly damaging	Het
Iqgap1	A	T	7: 80,759,839 (GRCm38)	N249K	probably benign	Het
Lamc1	A	G	1: 153,234,650 (GRCm38)	V1093A	possibly damaging	Het
Mfap3	A	G	11: 57,529,756 (GRCm38)	K188E	probably damaging	Het
N4bp2	T	A	5: 65,794,545 (GRCm38)	V431D	probably damaging	Het
Notch4	A	G	17: 34,576,471 (GRCm38)	T792A	probably benign	Het
Ntn4	A	G	10: 93,745,741 (GRCm38)	H592R	probably damaging	Het
Ofcc1	A	G	13: 40,208,841 (GRCm38)	C202R	probably benign	Het
Olfr13	A	G	6: 43,174,501 (GRCm38)	K172E	probably benign	Het
Olfr418	T	C	1: 173,270,994 (GRCm38)	I273T	probably benign	Het
Olfr476	T	C	7: 107,968,188 (GRCm38)	S264P	probably benign	Het
Olfr497	A	G	7: 108,422,933 (GRCm38)	M121V	probably damaging	Het
Olfr922	A	G	9: 38,815,713 (GRCm38)	D70G	probably benign	Het
Olfr938	A	T	9: 39,078,610 (GRCm38)	M45K	probably damaging	Het
Parpbp	G	A	10: 88,124,940 (GRCm38)	T228I	probably damaging	Het
Pcdhgb8	G	A	18: 37,763,703 (GRCm38)	V609M	probably damaging	Het
Pla2g4d	T	C	2: 120,270,349 (GRCm38)	N543S	probably damaging	Het
Puf60	A	G	15: 76,072,539 (GRCm38)		probably benign	Het
Rbm6	A	T	9: 107,852,896 (GRCm38)	D184E	probably damaging	Het
Rnase9	A	C	14: 51,038,979 (GRCm38)	S181A	probably benign	Het
Rnpc3	T	A	3: 113,616,831 (GRCm38)	R270S	probably damaging	Het
Rundc1	T	C	11: 101,431,548 (GRCm38)		probably null	Het
Ryr1	T	C	7: 29,052,015 (GRCm38)	S3715G	possibly damaging	Het
Serpina3k	T	G	12: 104,340,602 (GRCm38)	I31S	probably benign	Het
Sipa1l2	A	G	8: 125,469,860 (GRCm38)	F712L	probably damaging	Het
Slc22a29	A	G	19: 8,161,511 (GRCm38)	V529A	probably damaging	Het
Tdrd3	A	G	14: 87,458,803 (GRCm38)	N58S	probably benign	Het
Tmc2	C	T	2: 130,234,804 (GRCm38)	T350I	possibly damaging	Het
Tpst2	T	C	5: 112,307,678 (GRCm38)	C28R	probably benign	Het
Trbv21	A	T	6: 41,202,958 (GRCm38)	K69N	probably benign	Het
Trpm2	A	G	10: 77,935,876 (GRCm38)		probably null	Het
Ttn	A	G	2: 76,848,990 (GRCm38)	V10796A	unknown	Het
Ush2a	A	G	1: 188,911,661 (GRCm38)	T4407A	possibly damaging	Het
Vmn2r95	A	G	17: 18,451,963 (GRCm38)	H726R	probably benign	Het
Zfp777	A	G	6: 48,044,449 (GRCm38)	S80P	probably benign	Het

Other mutations in Scn3a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00953:Scn3a	APN	2	65,497,392 (GRCm38)	missense	probably benign	0.05
IGL01086:Scn3a	APN	2	65,470,159 (GRCm38)	missense	probably benign	0.27
IGL01141:Scn3a	APN	2	65,495,113 (GRCm38)	missense	possibly damaging	0.73
IGL01150:Scn3a	APN	2	65,497,365 (GRCm38)	splice site	probably null
IGL01564:Scn3a	APN	2	65,461,446 (GRCm38)	missense	probably damaging	1.00
IGL01594:Scn3a	APN	2	65,461,431 (GRCm38)	missense	probably damaging	1.00
IGL01751:Scn3a	APN	2	65,461,252 (GRCm38)	missense	possibly damaging	0.87
IGL01803:Scn3a	APN	2	65,521,783 (GRCm38)	unclassified	probably benign
IGL01822:Scn3a	APN	2	65,495,264 (GRCm38)	missense	probably damaging	1.00
IGL02063:Scn3a	APN	2	65,461,510 (GRCm38)	missense	probably damaging	1.00
IGL02142:Scn3a	APN	2	65,526,621 (GRCm38)	missense	possibly damaging	0.95
IGL02198:Scn3a	APN	2	65,508,489 (GRCm38)	missense	probably benign	0.12
IGL02501:Scn3a	APN	2	65,526,555 (GRCm38)	missense	possibly damaging	0.82
IGL02608:Scn3a	APN	2	65,524,166 (GRCm38)	nonsense	probably null
IGL02645:Scn3a	APN	2	65,514,527 (GRCm38)	missense	probably benign	0.12
IGL02653:Scn3a	APN	2	65,461,187 (GRCm38)	missense	probably damaging	1.00
IGL03077:Scn3a	APN	2	65,536,672 (GRCm38)	missense	probably damaging	0.99
IGL03099:Scn3a	APN	2	65,536,672 (GRCm38)	missense	probably damaging	0.99
IGL03299:Scn3a	APN	2	65,497,516 (GRCm38)	missense	probably benign	0.01
IGL03327:Scn3a	APN	2	65,536,672 (GRCm38)	missense	probably damaging	0.99
IGL03346:Scn3a	APN	2	65,536,672 (GRCm38)	missense	probably damaging	0.99
IGL03355:Scn3a	APN	2	65,460,568 (GRCm38)	missense	possibly damaging	0.91
curtsey	UTSW	2	65,464,836 (GRCm38)	missense	probably damaging	1.00
dip	UTSW	2	65,524,179 (GRCm38)	missense	probably benign	0.01
Regime	UTSW	2	65,524,850 (GRCm38)	missense	possibly damaging	0.93
Willpower	UTSW	2	65,525,754 (GRCm38)	missense	possibly damaging	0.92
R0019:Scn3a	UTSW	2	65,461,701 (GRCm38)	missense	probably damaging	1.00
R0316:Scn3a	UTSW	2	65,460,829 (GRCm38)	missense	probably damaging	1.00
R0374:Scn3a	UTSW	2	65,508,574 (GRCm38)	missense	probably damaging	0.97
R0414:Scn3a	UTSW	2	65,525,982 (GRCm38)	splice site	probably benign
R0609:Scn3a	UTSW	2	65,536,510 (GRCm38)	missense	probably damaging	0.96
R0613:Scn3a	UTSW	2	65,472,284 (GRCm38)	missense	possibly damaging	0.92
R0645:Scn3a	UTSW	2	65,524,850 (GRCm38)	missense	possibly damaging	0.93
R0665:Scn3a	UTSW	2	65,484,411 (GRCm38)	missense	probably null	0.00
R0667:Scn3a	UTSW	2	65,484,411 (GRCm38)	missense	probably null	0.00
R0710:Scn3a	UTSW	2	65,469,046 (GRCm38)	missense	probably damaging	0.99
R1202:Scn3a	UTSW	2	65,506,147 (GRCm38)	missense	probably benign	0.07
R1440:Scn3a	UTSW	2	65,529,441 (GRCm38)	missense	possibly damaging	0.95
R1447:Scn3a	UTSW	2	65,469,980 (GRCm38)	missense	probably damaging	1.00
R1564:Scn3a	UTSW	2	65,514,635 (GRCm38)	missense	probably damaging	0.98
R1595:Scn3a	UTSW	2	65,498,979 (GRCm38)	missense	probably damaging	0.99
R1775:Scn3a	UTSW	2	65,472,342 (GRCm38)	missense	probably damaging	1.00
R1781:Scn3a	UTSW	2	65,472,385 (GRCm38)	missense	probably damaging	1.00
R1822:Scn3a	UTSW	2	65,484,372 (GRCm38)	missense	probably damaging	1.00
R1924:Scn3a	UTSW	2	65,461,534 (GRCm38)	missense	probably damaging	1.00
R2061:Scn3a	UTSW	2	65,461,308 (GRCm38)	missense	probably damaging	1.00
R2070:Scn3a	UTSW	2	65,520,866 (GRCm38)	missense	possibly damaging	0.72
R2174:Scn3a	UTSW	2	65,507,206 (GRCm38)	missense	probably damaging	0.99
R2656:Scn3a	UTSW	2	65,526,518 (GRCm38)	missense	probably damaging	0.99
R2680:Scn3a	UTSW	2	65,536,536 (GRCm38)	missense	probably benign	0.04
R3882:Scn3a	UTSW	2	65,482,279 (GRCm38)	missense	probably benign	0.03
R4019:Scn3a	UTSW	2	65,525,951 (GRCm38)	intron	probably benign
R4106:Scn3a	UTSW	2	65,495,035 (GRCm38)	missense	probably benign	0.07
R4108:Scn3a	UTSW	2	65,495,035 (GRCm38)	missense	probably benign	0.07
R4109:Scn3a	UTSW	2	65,495,035 (GRCm38)	missense	probably benign	0.07
R4225:Scn3a	UTSW	2	65,536,427 (GRCm38)	missense	probably damaging	0.99
R4419:Scn3a	UTSW	2	65,466,960 (GRCm38)	missense	probably damaging	1.00
R4552:Scn3a	UTSW	2	65,524,179 (GRCm38)	missense	probably benign	0.01
R4687:Scn3a	UTSW	2	65,464,730 (GRCm38)	missense	possibly damaging	0.65
R4780:Scn3a	UTSW	2	65,506,193 (GRCm38)	missense	probably damaging	1.00
R4820:Scn3a	UTSW	2	65,461,278 (GRCm38)	missense	probably damaging	1.00
R4856:Scn3a	UTSW	2	65,461,032 (GRCm38)	missense	probably damaging	1.00
R4886:Scn3a	UTSW	2	65,461,032 (GRCm38)	missense	probably damaging	1.00
R4914:Scn3a	UTSW	2	65,461,455 (GRCm38)	missense	probably damaging	1.00
R4915:Scn3a	UTSW	2	65,461,455 (GRCm38)	missense	probably damaging	1.00
R4918:Scn3a	UTSW	2	65,461,455 (GRCm38)	missense	probably damaging	1.00
R5088:Scn3a	UTSW	2	65,472,299 (GRCm38)	missense	probably damaging	1.00
R5101:Scn3a	UTSW	2	65,461,506 (GRCm38)	missense	probably damaging	1.00
R5128:Scn3a	UTSW	2	65,508,518 (GRCm38)	missense	probably benign	0.08
R5132:Scn3a	UTSW	2	65,468,204 (GRCm38)	missense	probably benign	0.09
R5297:Scn3a	UTSW	2	65,469,034 (GRCm38)	missense	possibly damaging	0.83
R5595:Scn3a	UTSW	2	65,460,713 (GRCm38)	missense	probably benign
R5699:Scn3a	UTSW	2	65,507,264 (GRCm38)	missense	possibly damaging	0.54
R5730:Scn3a	UTSW	2	65,495,260 (GRCm38)	missense	probably benign	0.00
R5735:Scn3a	UTSW	2	65,484,459 (GRCm38)	missense	probably benign	0.09
R5735:Scn3a	UTSW	2	65,482,278 (GRCm38)	missense	probably damaging	0.98
R5855:Scn3a	UTSW	2	65,464,730 (GRCm38)	missense	possibly damaging	0.65
R5888:Scn3a	UTSW	2	65,497,398 (GRCm38)	missense	probably benign	0.06
R5898:Scn3a	UTSW	2	65,514,695 (GRCm38)	missense	probably damaging	0.96
R5935:Scn3a	UTSW	2	65,464,836 (GRCm38)	missense	probably damaging	1.00
R5970:Scn3a	UTSW	2	65,494,781 (GRCm38)	intron	probably benign
R6214:Scn3a	UTSW	2	65,495,036 (GRCm38)	missense	probably benign	0.29
R6215:Scn3a	UTSW	2	65,495,036 (GRCm38)	missense	probably benign	0.29
R6235:Scn3a	UTSW	2	65,461,335 (GRCm38)	missense	probably damaging	0.97
R6307:Scn3a	UTSW	2	65,472,341 (GRCm38)	missense	probably damaging	1.00
R6355:Scn3a	UTSW	2	65,461,299 (GRCm38)	missense	probably damaging	0.99
R6376:Scn3a	UTSW	2	65,461,499 (GRCm38)	missense	possibly damaging	0.88
R6517:Scn3a	UTSW	2	65,497,563 (GRCm38)	missense	possibly damaging	0.73
R6775:Scn3a	UTSW	2	65,521,815 (GRCm38)	missense	possibly damaging	0.82
R6893:Scn3a	UTSW	2	65,525,754 (GRCm38)	missense	possibly damaging	0.92
R6986:Scn3a	UTSW	2	65,508,618 (GRCm38)	missense	probably damaging	0.97
R7065:Scn3a	UTSW	2	65,464,855 (GRCm38)	missense	probably benign
R7078:Scn3a	UTSW	2	65,497,600 (GRCm38)	missense	probably damaging	1.00
R7146:Scn3a	UTSW	2	65,483,142 (GRCm38)	missense	probably damaging	1.00
R7294:Scn3a	UTSW	2	65,472,341 (GRCm38)	missense	probably damaging	1.00
R7352:Scn3a	UTSW	2	65,525,701 (GRCm38)	missense	possibly damaging	0.51
R7636:Scn3a	UTSW	2	65,497,689 (GRCm38)	missense	probably damaging	1.00
R7708:Scn3a	UTSW	2	65,483,168 (GRCm38)	missense	possibly damaging	0.47
R7733:Scn3a	UTSW	2	65,508,650 (GRCm38)	missense	probably benign	0.08
R7761:Scn3a	UTSW	2	65,529,454 (GRCm38)	missense	possibly damaging	0.95
R7792:Scn3a	UTSW	2	65,466,990 (GRCm38)	nonsense	probably null
R7828:Scn3a	UTSW	2	65,508,574 (GRCm38)	missense	probably damaging	0.97
R7875:Scn3a	UTSW	2	65,497,482 (GRCm38)	missense	probably damaging	1.00
R7884:Scn3a	UTSW	2	65,536,515 (GRCm38)	missense	probably damaging	0.96
R7958:Scn3a	UTSW	2	65,506,193 (GRCm38)	missense	probably damaging	1.00
R7965:Scn3a	UTSW	2	65,506,211 (GRCm38)	missense	probably damaging	1.00
R8171:Scn3a	UTSW	2	65,530,810 (GRCm38)	missense	possibly damaging	0.85
R8345:Scn3a	UTSW	2	65,498,991 (GRCm38)	missense	possibly damaging	0.86
R8356:Scn3a	UTSW	2	65,460,673 (GRCm38)	missense	probably benign	0.08
R8456:Scn3a	UTSW	2	65,460,673 (GRCm38)	missense	probably benign	0.08
R8527:Scn3a	UTSW	2	65,497,519 (GRCm38)	missense	probably damaging	0.99
R8688:Scn3a	UTSW	2	65,525,703 (GRCm38)	missense	possibly damaging	0.92
R8731:Scn3a	UTSW	2	65,468,163 (GRCm38)	nonsense	probably null
R8901:Scn3a	UTSW	2	65,521,908 (GRCm38)	missense	probably benign	0.00
R8910:Scn3a	UTSW	2	65,508,539 (GRCm38)	missense	probably damaging	1.00
R9011:Scn3a	UTSW	2	65,521,826 (GRCm38)	missense	possibly damaging	0.71
R9364:Scn3a	UTSW	2	65,461,252 (GRCm38)	missense	possibly damaging	0.87
R9460:Scn3a	UTSW	2	65,470,191 (GRCm38)	missense	probably damaging	1.00
R9496:Scn3a	UTSW	2	65,482,149 (GRCm38)	critical splice donor site	probably null
R9542:Scn3a	UTSW	2	65,536,516 (GRCm38)	missense	probably damaging	0.99
R9563:Scn3a	UTSW	2	65,461,251 (GRCm38)	missense	probably damaging	1.00
X0062:Scn3a	UTSW	2	65,524,847 (GRCm38)	nonsense	probably null
X0062:Scn3a	UTSW	2	65,467,001 (GRCm38)	missense	probably damaging	0.98
Z1177:Scn3a	UTSW	2	65,498,892 (GRCm38)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CACTGTGAGCACTCTGCCAATC -3'
(R):5'- ATCATAGAATAGCTCCCAAGAGAAG -3'

Sequencing Primer
(F):5'- GAGCACTCTGCCAATCATTTTTACTG -3'
(R):5'- GGAATGTCCTTAGTAACACACCATTC -3'

Posted On

2019-06-26