Mutagenetix > Incidental Mutations

Incidental Mutation 'R0062:Vps13a'

16242

Institutional Source

Beutler Lab

Gene Symbol

Vps13a

Ensembl Gene

ENSMUSG00000046230

Gene Name

vacuolar protein sorting 13A

Synonyms

4930516E05Rik, 4930543C13Rik, D330038K10Rik

MMRRC Submission

038354-MU

Accession Numbers

Ncbi RefSeq: NM_173028.4; MGI:2444304

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0062 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

16615366-16780933 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 16668690 bp

Zygosity

Heterozygous

Amino Acid Change

Histidine to Glutamine at position 1994 (H1994Q)

Ref Sequence

ENSEMBL: ENSMUSP00000153129 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000068156] [ENSMUST00000224149]

Predicted Effect

probably damaging
Transcript: ENSMUST00000068156
AA Change: H1994Q

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000068716
Gene: ENSMUSG00000046230
AA Change: H1994Q

Domain	Start	End	E-Value	Type
Pfam:Chorein_N	3	117	5.4e-38	PFAM
Pfam:VPS13	139	371	3.7e-64	PFAM
low complexity region	553	563	N/A	INTRINSIC
Pfam:VPS13_mid_rpt	567	791	1.4e-69	PFAM
Pfam:VPS13_mid_rpt	1138	1329	2e-10	PFAM
low complexity region	1367	1377	N/A	INTRINSIC
Blast:INB	1575	1855	1e-149	BLAST
Pfam:SHR-BD	2200	2449	1.3e-35	PFAM
low complexity region	2510	2521	N/A	INTRINSIC
low complexity region	2632	2648	N/A	INTRINSIC
low complexity region	2719	2731	N/A	INTRINSIC
Pfam:VPS13_C	2755	2935	8.9e-66	PFAM
Pfam:ATG_C	2938	3029	1.6e-16	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000223897

Predicted Effect

probably damaging
Transcript: ENSMUST00000224149
AA Change: H1994Q

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000224725

Predicted Effect

probably benign
Transcript: ENSMUST00000225233

Meta Mutation Damage Score

0.3284

Coding Region Coverage

1x: 90.3%
3x: 88.1%
10x: 83.4%
20x: 77.5%

Validation Efficiency

91% (72/79)

MGI Phenotype

Strain: 3531502
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene may control steps in the cycling of proteins through the trans-Golgi network to endosomes, lysosomes and the plasma membrane. Mutations in this gene cause the autosomal recessive disorder, chorea-acanthocytosis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]
PHENOTYPE: Aging mice homozygous for a knock-out allele display motor dysfunction and abnormal social interaction, hematologic anomalies including acanthocytosis, selective atrophy of the striatum with significant apoptosis and gliosis, and reduced homovanillic acid levels in midbrain. [provided by MGI curators]

Allele List at MGI

All alleles(8) : Targeted(3) Gene trapped(5)

Other mutations in this stock

Total: 55 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921513I03Rik	G	T	10: 120,778,606		probably benign	Het
Abi2	T	A	1: 60,453,725	N182K	probably benign	Het
Adam25	A	T	8: 40,754,792	H365L	probably damaging	Het
Ankfy1	T	A	11: 72,712,204	Y20N	probably damaging	Het
Arhgef28	A	T	13: 97,956,642	I977N	possibly damaging	Het
Armc4	T	A	18: 7,129,593		probably benign	Het
Cacna1b	A	G	2: 24,758,331	Y161H	probably damaging	Het
Cacna1c	T	C	6: 118,602,237	D1480G	probably damaging	Het
Chl1	A	T	6: 103,749,652	Y1143F	unknown	Het
Clk3	A	G	9: 57,752,166	M533T	probably damaging	Het
Clstn1	G	A	4: 149,634,796	V361M	probably damaging	Het
Cnbd1	A	G	4: 18,860,504	I414T	possibly damaging	Het
Commd3	A	T	2: 18,674,703		probably null	Het
Dnah8	T	A	17: 30,765,711	F3128I	probably damaging	Het
Dock1	A	G	7: 134,777,495		probably null	Het
Dpysl3	C	T	18: 43,333,876		probably null	Het
Ebf2	T	A	14: 67,238,540		probably benign	Het
F830045P16Rik	T	C	2: 129,463,704	E250G	possibly damaging	Het
Fmn2	A	T	1: 174,608,449		probably benign	Het
Fryl	T	C	5: 73,022,278	I2929V	probably benign	Het
Gm11232	T	A	4: 71,756,875	Q130L	possibly damaging	Het
Gna15	A	G	10: 81,512,405		probably null	Het
Gtf3c5	T	C	2: 28,572,186		probably benign	Het
Irs2	G	A	8: 11,005,723	T903I	possibly damaging	Het
Itga2	G	A	13: 114,870,496	S432L	possibly damaging	Het
Izumo1	A	G	7: 45,627,197	T395A	probably benign	Het
Kcnd2	G	A	6: 21,727,226	V593M	possibly damaging	Het
Kprp	T	C	3: 92,824,682	S354G	probably damaging	Het
Krt72	T	C	15: 101,786,008	K151E	probably damaging	Het
Letm2	A	T	8: 25,587,448		probably benign	Het
Lipe	A	G	7: 25,398,449	V23A	possibly damaging	Het
Mcc	C	G	18: 44,519,516		probably benign	Het
Mthfd1	G	A	12: 76,297,589		probably benign	Het
Nbeal1	C	A	1: 60,247,717	N899K	probably benign	Het
Olfr1223	T	C	2: 89,144,622	I134V	possibly damaging	Het
Olfr1338	T	C	4: 118,753,903	I212V	probably benign	Het
Pcdha1	T	A	18: 37,006,628	W437R	probably benign	Het
Pcdhga11	T	G	18: 37,808,475	I643S	probably benign	Het
Pik3r6	T	A	11: 68,528,809	Y149N	probably damaging	Het
Pja2	C	A	17: 64,308,971	V310L	probably damaging	Het
Ripor3	A	G	2: 167,984,438		probably benign	Het
Rpa2	C	A	4: 132,777,814	N251K	probably damaging	Het
Rttn	T	C	18: 89,010,966		probably null	Het
Ryr2	C	T	13: 11,869,116		probably null	Het
Scara3	T	C	14: 65,930,968	N400S	probably damaging	Het
Slc8b1	T	A	5: 120,521,863		probably null	Het
Slco1a4	G	A	6: 141,819,479	Q346*	probably null	Het
Stk32b	A	G	5: 37,461,448	S229P	probably damaging	Het
Syde2	A	G	3: 145,998,753	R487G	probably benign	Het
Tbc1d2b	T	C	9: 90,222,302		probably benign	Het
Ticrr	T	C	7: 79,667,906	V396A	probably benign	Het
Trrap	T	C	5: 144,782,193		probably benign	Het
Wdr36	T	G	18: 32,864,749	V820G	possibly damaging	Het
Wdr83	G	A	8: 85,079,827	T114I	possibly damaging	Het
Zfc3h1	A	G	10: 115,416,753	K1324E	probably benign	Het

Other mutations in Vps13a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00465:Vps13a	APN	19	16752175	missense	probably damaging	0.98
IGL00537:Vps13a	APN	19	16680045	missense	probably benign	0.03
IGL00562:Vps13a	APN	19	16734714	critical splice donor site	probably null
IGL00563:Vps13a	APN	19	16734714	critical splice donor site	probably null
IGL00579:Vps13a	APN	19	16707362	missense	probably benign	0.29
IGL00662:Vps13a	APN	19	16704540	missense	probably damaging	0.96
IGL00667:Vps13a	APN	19	16759676	missense	probably damaging	1.00
IGL01102:Vps13a	APN	19	16651417	critical splice donor site	probably null
IGL01139:Vps13a	APN	19	16640625	missense	probably damaging	0.99
IGL01142:Vps13a	APN	19	16687115	missense	possibly damaging	0.86
IGL01361:Vps13a	APN	19	16743007	missense	probably damaging	1.00
IGL01386:Vps13a	APN	19	16701152	missense	possibly damaging	0.87
IGL01593:Vps13a	APN	19	16762181	missense	probably damaging	0.98
IGL01700:Vps13a	APN	19	16744857	nonsense	probably null
IGL01767:Vps13a	APN	19	16663894	missense	probably damaging	1.00
IGL01782:Vps13a	APN	19	16754337	missense	probably damaging	0.98
IGL01808:Vps13a	APN	19	16710286	missense	probably damaging	1.00
IGL01812:Vps13a	APN	19	16715060	missense	probably benign
IGL01829:Vps13a	APN	19	16619443	missense	probably benign	0.01
IGL01893:Vps13a	APN	19	16663775	missense	probably damaging	1.00
IGL02222:Vps13a	APN	19	16682175	missense	probably benign	0.06
IGL02295:Vps13a	APN	19	16715042	splice site	probably benign
IGL02465:Vps13a	APN	19	16710941	missense	probably benign	0.11
IGL02492:Vps13a	APN	19	16647637	missense	probably damaging	1.00
IGL02581:Vps13a	APN	19	16655322	missense	probably benign	0.41
IGL02633:Vps13a	APN	19	16720408	missense	possibly damaging	0.82
IGL02641:Vps13a	APN	19	16698821	missense	probably benign	0.01
IGL02659:Vps13a	APN	19	16652699	missense	probably damaging	1.00
IGL02827:Vps13a	APN	19	16641634	missense	possibly damaging	0.91
IGL02943:Vps13a	APN	19	16663886	missense	probably damaging	1.00
IGL03057:Vps13a	APN	19	16668694	missense	probably damaging	1.00
IGL03077:Vps13a	APN	19	16710882	missense	probably benign
IGL03184:Vps13a	APN	19	16654370	missense	probably benign	0.00
eggs	UTSW	19	16701165	missense	probably damaging	1.00
excambio	UTSW	19	16745947	splice site	probably null
Faster	UTSW	19	16619485	missense	probably damaging	1.00
Ham	UTSW	19	16677969	missense	probably benign	0.08
interchange	UTSW	19	16668690	missense	probably damaging	1.00
PIT4377001:Vps13a	UTSW	19	16740901	missense	probably damaging	1.00
R0045:Vps13a	UTSW	19	16640810	nonsense	probably null
R0045:Vps13a	UTSW	19	16640810	nonsense	probably null
R0048:Vps13a	UTSW	19	16676140	missense	probably damaging	1.00
R0062:Vps13a	UTSW	19	16668690	missense	probably damaging	1.00
R0107:Vps13a	UTSW	19	16691824	missense	probably benign	0.03
R0135:Vps13a	UTSW	19	16780765	missense	probably damaging	1.00
R0138:Vps13a	UTSW	19	16660499	missense	possibly damaging	0.95
R0346:Vps13a	UTSW	19	16677969	missense	probably benign	0.08
R0359:Vps13a	UTSW	19	16641577	missense	probably damaging	0.99
R0530:Vps13a	UTSW	19	16655206	splice site	probably benign
R0541:Vps13a	UTSW	19	16704577	missense	probably benign	0.00
R0614:Vps13a	UTSW	19	16652694	missense	probably damaging	1.00
R0685:Vps13a	UTSW	19	16780741	missense	probably damaging	1.00
R0801:Vps13a	UTSW	19	16686656	splice site	probably benign
R0835:Vps13a	UTSW	19	16734882	splice site	probably null
R0848:Vps13a	UTSW	19	16698897	missense	probably damaging	1.00
R1114:Vps13a	UTSW	19	16750151	missense	probably benign	0.41
R1205:Vps13a	UTSW	19	16640541	missense	probably damaging	1.00
R1365:Vps13a	UTSW	19	16619446	missense	probably damaging	1.00
R1445:Vps13a	UTSW	19	16701238	nonsense	probably null
R1451:Vps13a	UTSW	19	16710864	missense	probably benign	0.01
R1479:Vps13a	UTSW	19	16750114	splice site	probably benign
R1533:Vps13a	UTSW	19	16701130	nonsense	probably null
R1600:Vps13a	UTSW	19	16666272	missense	probably benign	0.01
R1870:Vps13a	UTSW	19	16759952	missense	probably damaging	1.00
R1871:Vps13a	UTSW	19	16664664	missense	probably benign	0.01
R1959:Vps13a	UTSW	19	16677938	missense	possibly damaging	0.49
R1960:Vps13a	UTSW	19	16725631	missense	probably damaging	1.00
R1993:Vps13a	UTSW	19	16722458	missense	probably benign	0.07
R2257:Vps13a	UTSW	19	16682174	missense	possibly damaging	0.85
R2276:Vps13a	UTSW	19	16710426	missense	possibly damaging	0.47
R2326:Vps13a	UTSW	19	16743057	missense	possibly damaging	0.71
R2338:Vps13a	UTSW	19	16720453	missense	probably damaging	1.00
R2359:Vps13a	UTSW	19	16652679	splice site	probably benign
R2421:Vps13a	UTSW	19	16759671	missense	probably benign
R2847:Vps13a	UTSW	19	16703599	missense	probably damaging	0.98
R3081:Vps13a	UTSW	19	16664737	missense	probably benign	0.02
R3522:Vps13a	UTSW	19	16766493	splice site	probably benign
R3613:Vps13a	UTSW	19	16685402	missense	probably damaging	1.00
R3797:Vps13a	UTSW	19	16745947	splice site	probably null
R3874:Vps13a	UTSW	19	16744953	missense	probably benign	0.01
R4032:Vps13a	UTSW	19	16616899	missense	probably damaging	1.00
R4111:Vps13a	UTSW	19	16640628	missense	probably damaging	1.00
R4383:Vps13a	UTSW	19	16701165	missense	probably damaging	1.00
R4504:Vps13a	UTSW	19	16695502	missense	possibly damaging	0.93
R4578:Vps13a	UTSW	19	16682110	missense	probably damaging	0.98
R4587:Vps13a	UTSW	19	16640039	missense	probably damaging	1.00
R4588:Vps13a	UTSW	19	16640039	missense	probably damaging	1.00
R4605:Vps13a	UTSW	19	16640039	missense	probably damaging	1.00
R4714:Vps13a	UTSW	19	16749856	missense	probably benign	0.01
R4756:Vps13a	UTSW	19	16655216	missense	probably benign	0.01
R4831:Vps13a	UTSW	19	16677992	missense	probably benign	0.04
R5068:Vps13a	UTSW	19	16746058	missense	probably benign	0.01
R5070:Vps13a	UTSW	19	16654484	missense	probably benign
R5082:Vps13a	UTSW	19	16744893	missense	probably damaging	1.00
R5182:Vps13a	UTSW	19	16695499	missense	possibly damaging	0.81
R5189:Vps13a	UTSW	19	16685315	missense	probably damaging	1.00
R5283:Vps13a	UTSW	19	16677970	missense	probably damaging	0.96
R5294:Vps13a	UTSW	19	16641667	missense	probably damaging	1.00
R5304:Vps13a	UTSW	19	16710387	missense	possibly damaging	0.78
R5554:Vps13a	UTSW	19	16722411	missense	probably damaging	1.00
R5592:Vps13a	UTSW	19	16725571	missense	probably damaging	1.00
R5611:Vps13a	UTSW	19	16725572	missense	probably damaging	1.00
R5665:Vps13a	UTSW	19	16668690	missense	probably damaging	1.00
R5671:Vps13a	UTSW	19	16715100	missense	probably benign	0.03
R5684:Vps13a	UTSW	19	16699045	missense	probably benign	0.00
R5767:Vps13a	UTSW	19	16664564	missense	probably damaging	1.00
R5810:Vps13a	UTSW	19	16666324	missense	probably benign	0.00
R5866:Vps13a	UTSW	19	16680023	missense	probably benign	0.04
R5886:Vps13a	UTSW	19	16664562	missense	probably benign	0.01
R5933:Vps13a	UTSW	19	16660530	missense	probably benign	0.34
R5965:Vps13a	UTSW	19	16619028	splice site	probably null
R6259:Vps13a	UTSW	19	16687170	nonsense	probably null
R6346:Vps13a	UTSW	19	16682214	missense	possibly damaging	0.94
R6459:Vps13a	UTSW	19	16664018	missense	possibly damaging	0.56
R6485:Vps13a	UTSW	19	16680050	missense	probably damaging	0.99
R6520:Vps13a	UTSW	19	16725579	missense	probably damaging	1.00
R6644:Vps13a	UTSW	19	16744919	missense	possibly damaging	0.90
R6932:Vps13a	UTSW	19	16678075	missense	probably benign	0.01
R6934:Vps13a	UTSW	19	16676194	missense	probably damaging	1.00
R6951:Vps13a	UTSW	19	16723740	missense	probably benign	0.00
R7027:Vps13a	UTSW	19	16664664	missense	probably benign	0.01
R7126:Vps13a	UTSW	19	16710879	missense	probably benign
R7206:Vps13a	UTSW	19	16754298	missense	probably damaging	1.00
R7248:Vps13a	UTSW	19	16678042	missense	probably benign	0.25
R7252:Vps13a	UTSW	19	16661064	missense	probably benign	0.00
R7255:Vps13a	UTSW	19	16654339	critical splice donor site	probably null
R7382:Vps13a	UTSW	19	16619485	missense	probably damaging	1.00
R7422:Vps13a	UTSW	19	16750173	missense	probably damaging	1.00
R7425:Vps13a	UTSW	19	16723702	missense	probably benign	0.13
R7523:Vps13a	UTSW	19	16703789	missense	probably benign
R7586:Vps13a	UTSW	19	16647598	missense	probably benign	0.08
R7587:Vps13a	UTSW	19	16703789	missense	probably benign	0.00
R7593:Vps13a	UTSW	19	16725663	missense	probably damaging	1.00
R7637:Vps13a	UTSW	19	16750149	missense	probably benign	0.02
R7763:Vps13a	UTSW	19	16746000	missense	possibly damaging	0.95
R7813:Vps13a	UTSW	19	16651456	missense	possibly damaging	0.81
R7815:Vps13a	UTSW	19	16725572	missense	probably damaging	1.00
R7861:Vps13a	UTSW	19	16655304	missense	probably damaging	1.00
R7909:Vps13a	UTSW	19	16720430	nonsense	probably null
R7939:Vps13a	UTSW	19	16740791	missense	possibly damaging	0.94
R8108:Vps13a	UTSW	19	16640787	missense	probably damaging	1.00
R8123:Vps13a	UTSW	19	16647702	missense	probably benign	0.01
R8134:Vps13a	UTSW	19	16654354	missense	possibly damaging	0.71
R8168:Vps13a	UTSW	19	16749548	missense	probably benign	0.09
R8272:Vps13a	UTSW	19	16749845	critical splice donor site	probably null
R8293:Vps13a	UTSW	19	16668605	missense	possibly damaging	0.81
R8303:Vps13a	UTSW	19	16616906	missense	probably benign	0.00
R8383:Vps13a	UTSW	19	16723705	missense	possibly damaging	0.83
R8386:Vps13a	UTSW	19	16701119	critical splice donor site	probably null
R8433:Vps13a	UTSW	19	16741236	missense	possibly damaging	0.56
R8436:Vps13a	UTSW	19	16740793	missense	probably benign	0.10
R8450:Vps13a	UTSW	19	16654507	splice site	probably null
R8476:Vps13a	UTSW	19	16722457	missense	possibly damaging	0.60
R8501:Vps13a	UTSW	19	16682120	missense	probably benign	0.39
R8552:Vps13a	UTSW	19	16754320	missense	probably damaging	0.99
R8680:Vps13a	UTSW	19	16645906	missense	not run
X0061:Vps13a	UTSW	19	16645868	missense	probably benign	0.40
X0066:Vps13a	UTSW	19	16742553	missense	probably benign	0.33
Z1177:Vps13a	UTSW	19	16699113	critical splice acceptor site	probably null
Z31818:Vps13a	UTSW	19	16780754	missense	possibly damaging	0.94

Posted On

2013-01-20