Mutagenetix > Incidental Mutations

Incidental Mutation 'R0015:Cacna1d'

64915

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

038310-MU

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.850) question?

Stock #

R0015 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

30039939-30491455 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 30114971 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 804 (T804I)

Ref Sequence

ENSEMBL: ENSMUSP00000153293 (fasta)

Gene Model

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

AlphaFold

Q99246

Predicted Effect

probably benign
Transcript: ENSMUST00000112249
AA Change: T804I

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000107868
Gene: ENSMUSG00000015968
AA Change: T804I

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: T826I

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000107869
Gene: ENSMUSG00000015968
AA Change: T826I

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

probably benign
Transcript: ENSMUST00000223803
AA Change: T804I

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000224073

Predicted Effect

probably benign
Transcript: ENSMUST00000224198
AA Change: T824I

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

Predicted Effect

probably benign
Transcript: ENSMUST00000224395

Predicted Effect

probably benign
Transcript: ENSMUST00000224785
AA Change: T804I

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

Meta Mutation Damage Score

0.0727

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.1%
20x: 94.2%

Validation Efficiency

97% (71/73)

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: 65 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2410089E03Rik	G	A	15: 8,186,184	R408H	probably damaging	Het
A130050O07Rik	A	G	1: 137,928,656	Y23C	unknown	Het
Adcy3	G	A	12: 4,195,260		probably null	Het
Aldh6a1	G	A	12: 84,441,780	L86F	probably damaging	Het
Arl10	G	T	13: 54,575,957		probably benign	Het
Armc3	A	G	2: 19,296,321		probably null	Het
Astn2	T	G	4: 66,266,382		probably null	Het
Ccny	A	C	18: 9,316,682		probably benign	Het
Cdh5	C	T	8: 104,140,927	T612I	probably benign	Het
Cfap58	A	G	19: 48,029,100	M800V	probably benign	Het
Clrn1	A	T	3: 58,846,427	I171K	probably damaging	Het
Cnp	T	A	11: 100,578,908		probably null	Het
Col12a1	T	C	9: 79,651,385	T1933A	probably damaging	Het
Cwf19l2	A	G	9: 3,454,666	S660G	probably benign	Het
Dync1i2	C	A	2: 71,214,484	R13S	probably damaging	Het
Eps8l1	A	T	7: 4,477,557		probably benign	Het
Espn	T	C	4: 152,139,152	T188A	possibly damaging	Het
F2	T	C	2: 91,630,607	E260G	probably benign	Het
Fat4	T	A	3: 38,982,503	S3435T	probably damaging	Het
Fchsd1	A	G	18: 37,962,959	C533R	probably benign	Het
Fstl5	G	A	3: 76,322,191	V100M	probably damaging	Het
Gls2	T	G	10: 128,209,350	L572R	probably damaging	Het
Gm20939	A	T	17: 94,876,768	E281D	probably benign	Het
Gpr35	T	G	1: 92,983,232	L222W	probably damaging	Het
Hsf5	C	A	11: 87,657,335	H615N	probably benign	Het
Id2	C	T	12: 25,095,803	D70N	probably damaging	Het
Ints2	T	C	11: 86,249,287	T240A	probably damaging	Het
Kcnn3	A	C	3: 89,662,773	D631A	probably damaging	Het
Klhdc8a	A	G	1: 132,303,005	T203A	probably damaging	Het
Lama4	C	T	10: 39,075,436	T1059M	possibly damaging	Het
Lgals8	A	G	13: 12,447,298	L226P	probably damaging	Het
Lifr	T	A	15: 7,188,186		probably null	Het
Lonp1	T	A	17: 56,618,406	Q462L	probably benign	Het
Lypd1	A	G	1: 125,910,438	V48A	possibly damaging	Het
Mapkapk2	A	G	1: 131,097,326	I67T	possibly damaging	Het
Mbd3l1	A	T	9: 18,484,858	D93V	probably benign	Het
Mdh1b	T	C	1: 63,721,800		probably benign	Het
Myh7b	C	T	2: 155,622,286	P569L	probably damaging	Het
Ncapd3	C	A	9: 27,051,809	A470E	probably damaging	Het
Ndrg2	A	G	14: 51,910,445		probably benign	Het
Nprl2	A	T	9: 107,544,419	I209F	probably damaging	Het
Ntrk1	A	G	3: 87,791,750		probably benign	Het
Olfm2	T	C	9: 20,668,741	E268G	probably damaging	Het
Olfr884	T	A	9: 38,047,667	Y148*	probably null	Het
Pcf11	T	A	7: 92,658,317	H881L	probably benign	Het
Pde10a	A	G	17: 8,977,197	D640G	probably damaging	Het
Pde9a	G	A	17: 31,386,356		probably null	Het
Pianp	G	T	6: 125,001,540	G236V	probably damaging	Het
Polr2g	A	G	19: 8,793,652	I160T	probably damaging	Het
Ppp1r3a	A	G	6: 14,717,661	S1085P	possibly damaging	Het
Pter	G	A	2: 13,001,000	G328D	probably damaging	Het
Rad51	T	A	2: 119,116,327	M5K	probably benign	Het
Rbm43	T	A	2: 51,925,667	I181F	probably benign	Het
Rgs12	T	C	5: 35,022,776		probably benign	Het
Rnf213	A	C	11: 119,441,606	D2547A	possibly damaging	Het
Slc20a2	C	A	8: 22,535,345	A21E	probably damaging	Het
Stab2	A	G	10: 86,843,617	S2503P	probably benign	Het
Sv2b	A	T	7: 75,125,641	F479L	probably damaging	Het
Sybu	T	C	15: 44,673,500	R349G	probably damaging	Het
Tead3	T	C	17: 28,341,351	Y2C	probably damaging	Het
Tnrc6c	T	A	11: 117,721,458	N307K	probably damaging	Het
Ubxn11	C	G	4: 134,116,025		probably null	Het
Ust	T	C	10: 8,330,065		probably benign	Het
Vmn2r116	T	A	17: 23,401,849	N852K	probably benign	Het
Zgrf1	T	C	3: 127,555,397		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
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
R5383:Cacna1d	UTSW	14	30045279	missense	possibly damaging	0.51
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
R9444:Cacna1d	UTSW	14	30107784	critical splice donor site	probably null
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'- GCCTCCTGGAATTGCATTCACCTG -3'
(R):5'- ATGACCTGAGTGGCCTATCTCCTG -3'

Sequencing Primer
(F):5'- CGCTGACTTTAGGGAAGCAC -3'
(R):5'- TGCCTTCTGGATGAAGGAGAATC -3'

Posted On

2013-08-06