Mutagenetix > Incidental Mutations

Incidental Mutation 'R5383:Cacna1d'

424868

Institutional Source

Beutler Lab

Gene Symbol

Cacna1d

Ensembl Gene

ENSMUSG00000015968

Gene Name

calcium channel, voltage-dependent, L type, alpha 1D subunit

Synonyms

C79217, Cchl1a2, Cav1.3alpha1, Cchl1a, Cacnl1a2, D-LTCC, 8430418G19Rik

MMRRC Submission

042958-MU

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.836) question?

Stock #

R5383 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

30039939-30491455 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 30045279 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 1910 (D1910V)

Ref Sequence

ENSEMBL: ENSMUSP00000153293 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000067620] [ENSMUST00000112249] [ENSMUST00000112250] [ENSMUST00000223803] [ENSMUST00000224198] [ENSMUST00000224395] [ENSMUST00000224785]

AlphaFold

Q99246

Predicted Effect

probably benign
Transcript: ENSMUST00000067620

SMART Domains

Protein: ENSMUSP00000065542
Gene: ENSMUSG00000015970

Domain	Start	End	E-Value	Type
Pfam:GMC_oxred_N	43	341	2.4e-98	PFAM
Pfam:Lycopene_cycl	45	110	8.4e-8	PFAM
Pfam:GMC_oxred_C	431	569	2.5e-43	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000112249
AA Change: D1919V

PolyPhen 2 Score 0.296 (Sensitivity: 0.91; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000107868
Gene: ENSMUSG00000015968
AA Change: D1919V

Domain	Start	End	E-Value	Type
low complexity region	1	10	N/A	INTRINSIC
low complexity region	54	67	N/A	INTRINSIC
Pfam:Ion_trans	163	405	4.8e-59	PFAM
PDB:4DEY\|B	406	502	3e-38	PDB
low complexity region	503	517	N/A	INTRINSIC
Pfam:Ion_trans	557	751	5.5e-46	PFAM
low complexity region	766	781	N/A	INTRINSIC
low complexity region	819	840	N/A	INTRINSIC
Pfam:Ion_trans	921	1151	7.2e-51	PFAM
Pfam:Ion_trans	1239	1448	3.6e-67	PFAM
Pfam:PKD_channel	1285	1455	1.9e-9	PFAM
Blast:EFh	1469	1497	2e-9	BLAST
Ca_chan_IQ	1583	1617	5.05e-16	SMART
low complexity region	1649	1661	N/A	INTRINSIC
low complexity region	1722	1728	N/A	INTRINSIC
low complexity region	1830	1840	N/A	INTRINSIC
low complexity region	1885	1905	N/A	INTRINSIC
low complexity region	1921	1936	N/A	INTRINSIC
low complexity region	2122	2133	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000112250
AA Change: D1941V

PolyPhen 2 Score 0.089 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000107869
Gene: ENSMUSG00000015968
AA Change: D1941V

Domain	Start	End	E-Value	Type
low complexity region	76	89	N/A	INTRINSIC
Pfam:Ion_trans	147	439	5.6e-72	PFAM
low complexity region	473	482	N/A	INTRINSIC
low complexity region	525	539	N/A	INTRINSIC
Pfam:Ion_trans	544	784	2e-56	PFAM
low complexity region	788	803	N/A	INTRINSIC
low complexity region	841	862	N/A	INTRINSIC
Pfam:Ion_trans	907	1185	2.6e-63	PFAM
Pfam:Ion_trans	1226	1482	1.7e-70	PFAM
Pfam:PKD_channel	1306	1477	1.2e-9	PFAM
Pfam:GPHH	1484	1553	2.3e-38	PFAM
Ca_chan_IQ	1605	1639	5.05e-16	SMART
Pfam:CAC1F_C	1649	2165	1.1e-68	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000223573

Predicted Effect

probably benign
Transcript: ENSMUST00000223803
AA Change: D1919V

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

Predicted Effect

probably benign
Transcript: ENSMUST00000224198
AA Change: D1954V

PolyPhen 2 Score 0.025 (Sensitivity: 0.95; Specificity: 0.81)

Predicted Effect

probably benign
Transcript: ENSMUST00000224395

Predicted Effect

possibly damaging
Transcript: ENSMUST00000224785
AA Change: D1910V

PolyPhen 2 Score 0.511 (Sensitivity: 0.88; Specificity: 0.90)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000225353

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000225717

Meta Mutation Damage Score

0.1795

Coding Region Coverage

1x: 99.4%
3x: 98.8%
10x: 97.5%
20x: 96.0%

Validation Efficiency

97% (61/63)

MGI Phenotype

FUNCTION: This gene encodes a pore-forming subunit of the L-type, voltage-activated calcium channel family. These channels have been found to play a role in heart and smooth muscle contraction and in the transmission of auditory information. Homozygous knockout mice for this gene exhibit deafness and heart defects. These channels have also been linked to mitochondrial oxidative stress in a mouse model of Parkinson's disease. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Nov 2014]
PHENOTYPE: Homozygotes for targeted mutations exhibit small size, hypoinsulinemia, glucose intolerance, decreased number and size of pancreatic islets, deafness with degeneration of hair cells, bradycardia, and arrhythmia. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 62 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700010I14Rik	A	T	17: 8,992,700	Y227F	possibly damaging	Het
4921501E09Rik	T	C	17: 33,065,257	D857G	probably benign	Het
Aadac	T	C	3: 60,036,075		probably benign	Het
Abl2	G	A	1: 156,642,232	G918E	possibly damaging	Het
Acvr1c	T	C	2: 58,287,735	T241A	probably damaging	Het
Adck1	T	C	12: 88,455,603	V328A	probably benign	Het
Ano6	A	G	15: 95,916,037	I279V	probably benign	Het
AW551984	T	A	9: 39,590,698	Y704F	probably benign	Het
C1s1	T	C	6: 124,534,401	D321G	probably damaging	Het
Ccdc129	T	A	6: 55,978,290	L961H	probably benign	Het
Cdh5	A	G	8: 104,137,847	Q480R	probably benign	Het
Cdhr1	C	T	14: 37,089,007	V266M	possibly damaging	Het
Cdk5rap1	A	T	2: 154,350,835	V414D	possibly damaging	Het
Ctdnep1	T	A	11: 69,984,396		probably benign	Het
Cyfip2	T	C	11: 46,278,091	M212V	possibly damaging	Het
D130043K22Rik	G	A	13: 24,857,414	S273N	probably benign	Het
Ddi2	A	G	4: 141,684,852	S250P	probably damaging	Het
Dennd1b	A	G	1: 139,167,671	T486A	probably benign	Het
Disc1	A	G	8: 125,135,457	T523A	probably damaging	Het
Dmbx1	A	G	4: 115,918,145	S313P	probably damaging	Het
Dmpk	C	G	7: 19,088,019	L301V	probably benign	Het
Dnah11	T	C	12: 118,085,697	E1664G	probably damaging	Het
Dpysl3	A	T	18: 43,438,038	V57E	probably damaging	Het
Fam98a	C	T	17: 75,538,581	G390E	unknown	Het
Hook3	C	A	8: 26,118,989	R9L	probably benign	Het
Igkv4-80	A	C	6: 69,016,665	S81A	probably benign	Het
Impg2	A	G	16: 56,243,626	D298G	probably benign	Het
Inf2	T	A	12: 112,600,145	V48D	probably damaging	Het
Kcnh1	G	A	1: 192,505,691	G820D	probably benign	Het
Lsm14a	C	T	7: 34,389,364	A39T	possibly damaging	Het
Muc2	T	C	7: 141,753,719	C804R	probably damaging	Het
Nim1k	C	T	13: 119,727,799	V25M	probably benign	Het
Olfr1246	T	C	2: 89,591,113	M1V	probably null	Het
Olfr1484	T	A	19: 13,586,075	M257K	probably damaging	Het
Olfr741	T	A	14: 50,486,052	L198*	probably null	Het
Olfr780	A	G	10: 129,322,336	T238A	probably damaging	Het
Otx1	C	A	11: 21,997,037	A91S	probably damaging	Het
Pitrm1	T	A	13: 6,577,432	H856Q	probably damaging	Het
Pkd1	T	C	17: 24,574,375	C1679R	probably benign	Het
Pkp4	T	A	2: 59,310,273	L441*	probably null	Het
Ppp4r4	T	C	12: 103,584,168	F284L	probably benign	Het
Ptprt	T	A	2: 161,698,049	K769M	probably damaging	Het
Rbm12	G	T	2: 156,103,365		probably benign	Het
Rpf1	T	C	3: 146,519,391	D94G	possibly damaging	Het
Scap	G	T	9: 110,374,529	K310N	probably damaging	Het
Smpd2	C	T	10: 41,488,702		probably benign	Het
Sp110	TC	TCC	1: 85,591,569		probably null	Het
Specc1l	T	A	10: 75,246,705	I662N	possibly damaging	Het
Sptan1	T	A	2: 30,011,328	V1496D	probably damaging	Het
Srrm4	T	C	5: 116,471,260		probably benign	Het
Taf2	A	G	15: 55,049,419	I515T	possibly damaging	Het
Tdrd3	C	T	14: 87,480,791	Q203*	probably null	Het
Tfap2b	A	T	1: 19,226,498	M222L	probably benign	Het
Tmem43	G	A	6: 91,473,890	A2T	probably benign	Het
Trav9-1	T	A	14: 53,488,376	I49N	probably benign	Het
Trim23	T	G	13: 104,198,697	N410K	probably damaging	Het
Ttbk1	T	C	17: 46,467,416	T567A	probably damaging	Het
Unc79	A	G	12: 103,104,627	N1081S	possibly damaging	Het
Zfp451	A	C	1: 33,813,806	I9R	probably damaging	Het
Zfp563	T	A	17: 33,104,707	M92K	probably benign	Het
Zfp618	G	A	4: 63,095,492	G198D	probably benign	Het
Zfp637	G	T	6: 117,843,309		probably benign	Het

Other mutations in Cacna1d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00494:Cacna1d	APN	14	30096950	missense	probably damaging	0.97
IGL00857:Cacna1d	APN	14	30350681	missense	possibly damaging	0.83
IGL01015:Cacna1d	APN	14	30051742	splice site	probably benign
IGL01420:Cacna1d	APN	14	30051638	missense	probably benign	0.01
IGL01470:Cacna1d	APN	14	30099142	missense	probably damaging	0.99
IGL01560:Cacna1d	APN	14	30099206	missense	probably benign	0.00
IGL01617:Cacna1d	APN	14	30102371	missense	probably damaging	1.00
IGL01820:Cacna1d	APN	14	30042866	missense	possibly damaging	0.79
IGL01948:Cacna1d	APN	14	30124794	missense	probably damaging	1.00
IGL02702:Cacna1d	APN	14	30123533	nonsense	probably null
IGL02864:Cacna1d	APN	14	30051706	missense	probably benign	0.10
IGL03082:Cacna1d	APN	14	30099233	missense	probably damaging	1.00
Brisk	UTSW	14	30171314	missense	possibly damaging	0.91
Troppo	UTSW	14	30123454	missense	probably damaging	1.00
PIT4651001:Cacna1d	UTSW	14	30178645	missense	probably damaging	1.00
R0015:Cacna1d	UTSW	14	30114971	missense	probably benign	0.00
R0015:Cacna1d	UTSW	14	30114971	missense	probably benign	0.00
R0033:Cacna1d	UTSW	14	30105489	missense	probably damaging	0.99
R0047:Cacna1d	UTSW	14	30346790	splice site	probably benign
R0047:Cacna1d	UTSW	14	30346790	splice site	probably benign
R0051:Cacna1d	UTSW	14	30111095	missense	probably damaging	1.00
R0051:Cacna1d	UTSW	14	30111095	missense	probably damaging	1.00
R0067:Cacna1d	UTSW	14	30075010	unclassified	probably benign
R0067:Cacna1d	UTSW	14	30075010	unclassified	probably benign
R0238:Cacna1d	UTSW	14	30123496	missense	probably benign	0.29
R0238:Cacna1d	UTSW	14	30123496	missense	probably benign	0.29
R0239:Cacna1d	UTSW	14	30123496	missense	probably benign	0.29
R0239:Cacna1d	UTSW	14	30123496	missense	probably benign	0.29
R0240:Cacna1d	UTSW	14	30096969	missense	probably benign	0.00
R0240:Cacna1d	UTSW	14	30096969	missense	probably benign	0.00
R0284:Cacna1d	UTSW	14	30072105	missense	probably damaging	1.00
R0416:Cacna1d	UTSW	14	30100688	splice site	probably benign
R0427:Cacna1d	UTSW	14	30346817	missense	probably damaging	0.99
R0517:Cacna1d	UTSW	14	30179275	missense	probably damaging	1.00
R0639:Cacna1d	UTSW	14	30171294	critical splice donor site	probably null
R0727:Cacna1d	UTSW	14	30130115	critical splice donor site	probably null
R0732:Cacna1d	UTSW	14	30042920	missense	probably damaging	0.99
R0843:Cacna1d	UTSW	14	30124871	missense	probably damaging	1.00
R0900:Cacna1d	UTSW	14	30111082	missense	probably damaging	1.00
R1278:Cacna1d	UTSW	14	30178703	missense	probably damaging	1.00
R1340:Cacna1d	UTSW	14	30072067	missense	probably damaging	0.96
R1527:Cacna1d	UTSW	14	30107796	missense	probably damaging	1.00
R1711:Cacna1d	UTSW	14	30066056	missense	probably damaging	1.00
R1736:Cacna1d	UTSW	14	30089863	missense	probably damaging	1.00
R1763:Cacna1d	UTSW	14	30099196	missense	probably benign	0.25
R2034:Cacna1d	UTSW	14	30089863	missense	probably damaging	1.00
R2086:Cacna1d	UTSW	14	30047357	missense	possibly damaging	0.83
R2126:Cacna1d	UTSW	14	30123163	missense	probably damaging	1.00
R2218:Cacna1d	UTSW	14	30123091	missense	probably damaging	1.00
R2219:Cacna1d	UTSW	14	30042090	missense	probably damaging	1.00
R2262:Cacna1d	UTSW	14	30491016	missense	possibly damaging	0.46
R2291:Cacna1d	UTSW	14	30042342	missense	probably damaging	1.00
R2399:Cacna1d	UTSW	14	30052487	missense	probably benign	0.34
R2424:Cacna1d	UTSW	14	30049023	missense	probably damaging	0.96
R2568:Cacna1d	UTSW	14	30082511	missense	probably damaging	0.99
R4038:Cacna1d	UTSW	14	30066083	missense	probably damaging	0.96
R4509:Cacna1d	UTSW	14	30096971	missense	probably damaging	1.00
R4649:Cacna1d	UTSW	14	30095408	missense	probably benign
R4650:Cacna1d	UTSW	14	30095408	missense	probably benign
R4652:Cacna1d	UTSW	14	30095408	missense	probably benign
R5009:Cacna1d	UTSW	14	30079332	missense	probably damaging	1.00
R5058:Cacna1d	UTSW	14	30114244	nonsense	probably null
R5063:Cacna1d	UTSW	14	30051383	missense	probably benign
R5138:Cacna1d	UTSW	14	30490972	missense	probably benign
R5151:Cacna1d	UTSW	14	30123323	missense	probably damaging	1.00
R5278:Cacna1d	UTSW	14	30352924	critical splice donor site	probably null
R5286:Cacna1d	UTSW	14	30350725	missense	possibly damaging	0.69
R5313:Cacna1d	UTSW	14	30346841	missense	probably benign	0.38
R5387:Cacna1d	UTSW	14	30100751	missense	probably damaging	1.00
R5514:Cacna1d	UTSW	14	30350833	nonsense	probably null
R5524:Cacna1d	UTSW	14	30042129	missense	probably benign	0.01
R5663:Cacna1d	UTSW	14	30123340	missense	probably damaging	1.00
R5712:Cacna1d	UTSW	14	30074997	missense	probably damaging	1.00
R5796:Cacna1d	UTSW	14	30066116	missense	probably damaging	1.00
R5906:Cacna1d	UTSW	14	30096960	missense	probably damaging	1.00
R5923:Cacna1d	UTSW	14	30111148	missense	probably damaging	1.00
R5936:Cacna1d	UTSW	14	30171314	missense	possibly damaging	0.91
R5938:Cacna1d	UTSW	14	30103735	missense	probably damaging	1.00
R6041:Cacna1d	UTSW	14	30042357	missense	probably damaging	1.00
R6432:Cacna1d	UTSW	14	30123454	missense	probably damaging	1.00
R6486:Cacna1d	UTSW	14	30114233	missense	probably benign	0.01
R6600:Cacna1d	UTSW	14	30114235	missense	probably benign	0.15
R6661:Cacna1d	UTSW	14	30089875	missense	probably damaging	1.00
R6753:Cacna1d	UTSW	14	30042786	missense	probably damaging	1.00
R6804:Cacna1d	UTSW	14	30051665	missense	probably benign	0.00
R6851:Cacna1d	UTSW	14	30042782	missense	probably damaging	1.00
R6863:Cacna1d	UTSW	14	30075852	missense	probably damaging	1.00
R6916:Cacna1d	UTSW	14	30095364	missense	probably damaging	1.00
R6925:Cacna1d	UTSW	14	30051637	missense	probably benign
R7066:Cacna1d	UTSW	14	30352978	intron	probably benign
R7188:Cacna1d	UTSW	14	30089833	missense	probably benign
R7242:Cacna1d	UTSW	14	30178706	missense	probably benign	0.00
R7249:Cacna1d	UTSW	14	30142703	missense	probably damaging	1.00
R7250:Cacna1d	UTSW	14	30075151	missense	probably damaging	1.00
R7274:Cacna1d	UTSW	14	30142643	missense	probably damaging	1.00
R7336:Cacna1d	UTSW	14	30045282	missense	probably benign	0.18
R7343:Cacna1d	UTSW	14	30123057	missense	probably benign	0.02
R7411:Cacna1d	UTSW	14	30352990	start codon destroyed	probably null
R7461:Cacna1d	UTSW	14	30066163	missense	probably benign	0.05
R7534:Cacna1d	UTSW	14	30079362	missense	probably damaging	1.00
R7613:Cacna1d	UTSW	14	30066163	missense	probably benign	0.05
R7661:Cacna1d	UTSW	14	30047220	missense	probably benign	0.07
R7754:Cacna1d	UTSW	14	30075852	missense	probably damaging	1.00
R7759:Cacna1d	UTSW	14	30099188	missense	probably benign	0.01
R7784:Cacna1d	UTSW	14	30123439	missense	probably damaging	1.00
R7808:Cacna1d	UTSW	14	30111069	missense	probably damaging	1.00
R7965:Cacna1d	UTSW	14	30047313	nonsense	probably null
R8225:Cacna1d	UTSW	14	30123033	missense	probably benign	0.23
R8259:Cacna1d	UTSW	14	30051518	missense	probably benign
R8348:Cacna1d	UTSW	14	30102407	missense	probably damaging	1.00
R8448:Cacna1d	UTSW	14	30102407	missense	probably damaging	1.00
R8822:Cacna1d	UTSW	14	30178735	missense	probably benign	0.02
R8848:Cacna1d	UTSW	14	30123326	missense	possibly damaging	0.89
R9122:Cacna1d	UTSW	14	30123445	missense	probably damaging	1.00
R9122:Cacna1d	UTSW	14	30130168	missense	probably benign	0.00
R9169:Cacna1d	UTSW	14	30074916	missense	probably damaging	1.00
R9199:Cacna1d	UTSW	14	30042936	missense	probably benign	0.26
R9203:Cacna1d	UTSW	14	30051712	missense	probably benign	0.04
R9263:Cacna1d	UTSW	14	30074968	missense	probably damaging	1.00
R9346:Cacna1d	UTSW	14	30096923	missense	possibly damaging	0.86
Z1176:Cacna1d	UTSW	14	30111116	missense	probably benign	0.15
Z1176:Cacna1d	UTSW	14	30179188	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- GTGCAACTCCAGCAGAATGG -3'
(R):5'- CTCTTGGATGAAGCATGTGGC -3'

Sequencing Primer
(F):5'- CCTGGGGGATCTACCAGGAAG -3'
(R):5'- AAGCATGTGGCCTGCTTC -3'

Posted On

2016-08-04