Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02641:Vps13a'

301734

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Vps13a

Ensembl Gene

ENSMUSG00000046230

Gene Name

vacuolar protein sorting 13A

Synonyms

4930543C13Rik, D330038K10Rik, 4930516E05Rik

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

IGL02641

Quality Score

Status

Chromosome

Chromosomal Location

16592730-16758297 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 16676185 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Leucine at position 1263 (M1263L)

Ref Sequence

ENSEMBL: ENSMUSP00000068716 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000068156
AA Change: M1263L

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

SMART Domains

Protein: ENSMUSP00000068716
Gene: ENSMUSG00000046230
AA Change: M1263L

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

probably benign
Transcript: ENSMUST00000224149
AA Change: M1263L

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

Coding Region Coverage

Validation Efficiency

MGI Phenotype

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: 30 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3100002H09Rik	A	T	4: 124,504,510 (GRCm39)	M14K	unknown	Het
Arhgap24	T	C	5: 103,040,386 (GRCm39)	V441A	probably damaging	Het
Cdv3	G	T	9: 103,241,223 (GRCm39)	Q115K	probably damaging	Het
Clstn1	G	T	4: 149,713,968 (GRCm39)	G207C	probably null	Het
Col28a1	A	T	6: 8,014,794 (GRCm39)	Y870*	probably null	Het
Creb3	A	C	4: 43,563,311 (GRCm39)	H136P	probably benign	Het
Dcaf17	G	A	2: 70,912,375 (GRCm39)	C320Y	probably damaging	Het
Fbl	T	C	7: 27,874,471 (GRCm39)	S66P	probably damaging	Het
Fgfrl1	C	A	5: 108,853,731 (GRCm39)	S279R	probably damaging	Het
Gdpgp1	C	T	7: 79,888,796 (GRCm39)	R276*	probably null	Het
Hcfc2	A	G	10: 82,538,383 (GRCm39)	Y140C	probably damaging	Het
Ighg3	A	G	12: 113,323,818 (GRCm39)	I190T	unknown	Het
Itgav	T	C	2: 83,598,689 (GRCm39)		probably benign	Het
Lce1c	C	A	3: 92,587,845 (GRCm39)		probably benign	Het
Ldoc1	G	A	X: 60,753,419 (GRCm39)	C35Y	probably damaging	Het
Lrp10	T	A	14: 54,706,068 (GRCm39)	C419*	probably null	Het
Micall2	T	C	5: 139,705,094 (GRCm39)	D80G	probably damaging	Het
Or5b21	T	A	19: 12,839,566 (GRCm39)	C142*	probably null	Het
Pde3b	C	T	7: 114,130,052 (GRCm39)	T869I	probably damaging	Het
Pip5k1c	C	A	10: 81,153,155 (GRCm39)		probably null	Het
Pkhd1	G	A	1: 20,628,976 (GRCm39)	T657I	possibly damaging	Het
Pnisr	A	G	4: 21,860,908 (GRCm39)	N197S	probably benign	Het
Rpl21-ps4	G	A	14: 11,227,661 (GRCm38)		noncoding transcript	Het
Rtn4rl1	A	C	11: 75,156,650 (GRCm39)	T361P	probably damaging	Het
Spaca9	C	A	2: 28,585,963 (GRCm39)	E34*	probably null	Het
Trip10	T	A	17: 57,569,411 (GRCm39)	D478E	probably benign	Het
Tsc22d2	A	G	3: 58,323,576 (GRCm39)	D156G	probably damaging	Het
Ufc1	T	C	1: 171,117,764 (GRCm39)	D50G	probably damaging	Het
Vmn1r202	T	G	13: 22,686,274 (GRCm39)	I48L	probably benign	Het
Vmn2r111	A	T	17: 22,792,205 (GRCm39)	V17E	possibly damaging	Het

Other mutations in Vps13a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00465:Vps13a	APN	19	16,729,539 (GRCm39)	missense	probably damaging	0.98
IGL00537:Vps13a	APN	19	16,657,409 (GRCm39)	missense	probably benign	0.03
IGL00562:Vps13a	APN	19	16,712,078 (GRCm39)	critical splice donor site	probably null
IGL00563:Vps13a	APN	19	16,712,078 (GRCm39)	critical splice donor site	probably null
IGL00579:Vps13a	APN	19	16,684,726 (GRCm39)	missense	probably benign	0.29
IGL00662:Vps13a	APN	19	16,681,904 (GRCm39)	missense	probably damaging	0.96
IGL00667:Vps13a	APN	19	16,737,040 (GRCm39)	missense	probably damaging	1.00
IGL01102:Vps13a	APN	19	16,628,781 (GRCm39)	critical splice donor site	probably null
IGL01139:Vps13a	APN	19	16,617,989 (GRCm39)	missense	probably damaging	0.99
IGL01142:Vps13a	APN	19	16,664,479 (GRCm39)	missense	possibly damaging	0.86
IGL01361:Vps13a	APN	19	16,720,371 (GRCm39)	missense	probably damaging	1.00
IGL01386:Vps13a	APN	19	16,678,516 (GRCm39)	missense	possibly damaging	0.87
IGL01593:Vps13a	APN	19	16,739,545 (GRCm39)	missense	probably damaging	0.98
IGL01700:Vps13a	APN	19	16,722,221 (GRCm39)	nonsense	probably null
IGL01767:Vps13a	APN	19	16,641,258 (GRCm39)	missense	probably damaging	1.00
IGL01782:Vps13a	APN	19	16,731,701 (GRCm39)	missense	probably damaging	0.98
IGL01808:Vps13a	APN	19	16,687,650 (GRCm39)	missense	probably damaging	1.00
IGL01812:Vps13a	APN	19	16,692,424 (GRCm39)	missense	probably benign
IGL01829:Vps13a	APN	19	16,596,807 (GRCm39)	missense	probably benign	0.01
IGL01893:Vps13a	APN	19	16,641,139 (GRCm39)	missense	probably damaging	1.00
IGL02222:Vps13a	APN	19	16,659,539 (GRCm39)	missense	probably benign	0.06
IGL02295:Vps13a	APN	19	16,692,406 (GRCm39)	splice site	probably benign
IGL02465:Vps13a	APN	19	16,688,305 (GRCm39)	missense	probably benign	0.11
IGL02492:Vps13a	APN	19	16,625,001 (GRCm39)	missense	probably damaging	1.00
IGL02581:Vps13a	APN	19	16,632,686 (GRCm39)	missense	probably benign	0.41
IGL02633:Vps13a	APN	19	16,697,772 (GRCm39)	missense	possibly damaging	0.82
IGL02659:Vps13a	APN	19	16,630,063 (GRCm39)	missense	probably damaging	1.00
IGL02827:Vps13a	APN	19	16,618,998 (GRCm39)	missense	possibly damaging	0.91
IGL02943:Vps13a	APN	19	16,641,250 (GRCm39)	missense	probably damaging	1.00
IGL03057:Vps13a	APN	19	16,646,058 (GRCm39)	missense	probably damaging	1.00
IGL03077:Vps13a	APN	19	16,688,246 (GRCm39)	missense	probably benign
IGL03184:Vps13a	APN	19	16,631,734 (GRCm39)	missense	probably benign	0.00
eggs	UTSW	19	16,678,529 (GRCm39)	missense	probably damaging	1.00
excambio	UTSW	19	16,723,311 (GRCm39)	splice site	probably null
Faster	UTSW	19	16,596,849 (GRCm39)	missense	probably damaging	1.00
Ham	UTSW	19	16,655,333 (GRCm39)	missense	probably benign	0.08
interchange	UTSW	19	16,646,054 (GRCm39)	missense	probably damaging	1.00
PIT4377001:Vps13a	UTSW	19	16,718,265 (GRCm39)	missense	probably damaging	1.00
R0045:Vps13a	UTSW	19	16,618,174 (GRCm39)	nonsense	probably null
R0045:Vps13a	UTSW	19	16,618,174 (GRCm39)	nonsense	probably null
R0048:Vps13a	UTSW	19	16,653,504 (GRCm39)	missense	probably damaging	1.00
R0062:Vps13a	UTSW	19	16,646,054 (GRCm39)	missense	probably damaging	1.00
R0062:Vps13a	UTSW	19	16,646,054 (GRCm39)	missense	probably damaging	1.00
R0107:Vps13a	UTSW	19	16,669,188 (GRCm39)	missense	probably benign	0.03
R0135:Vps13a	UTSW	19	16,758,129 (GRCm39)	missense	probably damaging	1.00
R0138:Vps13a	UTSW	19	16,637,863 (GRCm39)	missense	possibly damaging	0.95
R0346:Vps13a	UTSW	19	16,655,333 (GRCm39)	missense	probably benign	0.08
R0359:Vps13a	UTSW	19	16,618,941 (GRCm39)	missense	probably damaging	0.99
R0530:Vps13a	UTSW	19	16,632,570 (GRCm39)	splice site	probably benign
R0541:Vps13a	UTSW	19	16,681,941 (GRCm39)	missense	probably benign	0.00
R0614:Vps13a	UTSW	19	16,630,058 (GRCm39)	missense	probably damaging	1.00
R0685:Vps13a	UTSW	19	16,758,105 (GRCm39)	missense	probably damaging	1.00
R0801:Vps13a	UTSW	19	16,664,020 (GRCm39)	splice site	probably benign
R0835:Vps13a	UTSW	19	16,712,246 (GRCm39)	splice site	probably null
R0848:Vps13a	UTSW	19	16,676,261 (GRCm39)	missense	probably damaging	1.00
R1114:Vps13a	UTSW	19	16,727,515 (GRCm39)	missense	probably benign	0.41
R1205:Vps13a	UTSW	19	16,617,905 (GRCm39)	missense	probably damaging	1.00
R1365:Vps13a	UTSW	19	16,596,810 (GRCm39)	missense	probably damaging	1.00
R1445:Vps13a	UTSW	19	16,678,602 (GRCm39)	nonsense	probably null
R1451:Vps13a	UTSW	19	16,688,228 (GRCm39)	missense	probably benign	0.01
R1479:Vps13a	UTSW	19	16,727,478 (GRCm39)	splice site	probably benign
R1533:Vps13a	UTSW	19	16,678,494 (GRCm39)	nonsense	probably null
R1600:Vps13a	UTSW	19	16,643,636 (GRCm39)	missense	probably benign	0.01
R1870:Vps13a	UTSW	19	16,737,316 (GRCm39)	missense	probably damaging	1.00
R1871:Vps13a	UTSW	19	16,642,028 (GRCm39)	missense	probably benign	0.01
R1959:Vps13a	UTSW	19	16,655,302 (GRCm39)	missense	possibly damaging	0.49
R1960:Vps13a	UTSW	19	16,702,995 (GRCm39)	missense	probably damaging	1.00
R1993:Vps13a	UTSW	19	16,699,822 (GRCm39)	missense	probably benign	0.07
R2257:Vps13a	UTSW	19	16,659,538 (GRCm39)	missense	possibly damaging	0.85
R2276:Vps13a	UTSW	19	16,687,790 (GRCm39)	missense	possibly damaging	0.47
R2326:Vps13a	UTSW	19	16,720,421 (GRCm39)	missense	possibly damaging	0.71
R2338:Vps13a	UTSW	19	16,697,817 (GRCm39)	missense	probably damaging	1.00
R2359:Vps13a	UTSW	19	16,630,043 (GRCm39)	splice site	probably benign
R2421:Vps13a	UTSW	19	16,737,035 (GRCm39)	missense	probably benign
R2847:Vps13a	UTSW	19	16,680,963 (GRCm39)	missense	probably damaging	0.98
R3081:Vps13a	UTSW	19	16,642,101 (GRCm39)	missense	probably benign	0.02
R3522:Vps13a	UTSW	19	16,743,857 (GRCm39)	splice site	probably benign
R3613:Vps13a	UTSW	19	16,662,766 (GRCm39)	missense	probably damaging	1.00
R3797:Vps13a	UTSW	19	16,723,311 (GRCm39)	splice site	probably null
R3874:Vps13a	UTSW	19	16,722,317 (GRCm39)	missense	probably benign	0.01
R4032:Vps13a	UTSW	19	16,594,263 (GRCm39)	missense	probably damaging	1.00
R4111:Vps13a	UTSW	19	16,617,992 (GRCm39)	missense	probably damaging	1.00
R4383:Vps13a	UTSW	19	16,678,529 (GRCm39)	missense	probably damaging	1.00
R4504:Vps13a	UTSW	19	16,672,866 (GRCm39)	missense	possibly damaging	0.93
R4578:Vps13a	UTSW	19	16,659,474 (GRCm39)	missense	probably damaging	0.98
R4587:Vps13a	UTSW	19	16,617,403 (GRCm39)	missense	probably damaging	1.00
R4588:Vps13a	UTSW	19	16,617,403 (GRCm39)	missense	probably damaging	1.00
R4605:Vps13a	UTSW	19	16,617,403 (GRCm39)	missense	probably damaging	1.00
R4714:Vps13a	UTSW	19	16,727,220 (GRCm39)	missense	probably benign	0.01
R4756:Vps13a	UTSW	19	16,632,580 (GRCm39)	missense	probably benign	0.01
R4831:Vps13a	UTSW	19	16,655,356 (GRCm39)	missense	probably benign	0.04
R5068:Vps13a	UTSW	19	16,723,422 (GRCm39)	missense	probably benign	0.01
R5070:Vps13a	UTSW	19	16,631,848 (GRCm39)	missense	probably benign
R5082:Vps13a	UTSW	19	16,722,257 (GRCm39)	missense	probably damaging	1.00
R5182:Vps13a	UTSW	19	16,672,863 (GRCm39)	missense	possibly damaging	0.81
R5189:Vps13a	UTSW	19	16,662,679 (GRCm39)	missense	probably damaging	1.00
R5283:Vps13a	UTSW	19	16,655,334 (GRCm39)	missense	probably damaging	0.96
R5294:Vps13a	UTSW	19	16,619,031 (GRCm39)	missense	probably damaging	1.00
R5304:Vps13a	UTSW	19	16,687,751 (GRCm39)	missense	possibly damaging	0.78
R5554:Vps13a	UTSW	19	16,699,775 (GRCm39)	missense	probably damaging	1.00
R5592:Vps13a	UTSW	19	16,702,935 (GRCm39)	missense	probably damaging	1.00
R5611:Vps13a	UTSW	19	16,702,936 (GRCm39)	missense	probably damaging	1.00
R5665:Vps13a	UTSW	19	16,646,054 (GRCm39)	missense	probably damaging	1.00
R5671:Vps13a	UTSW	19	16,692,464 (GRCm39)	missense	probably benign	0.03
R5684:Vps13a	UTSW	19	16,676,409 (GRCm39)	missense	probably benign	0.00
R5767:Vps13a	UTSW	19	16,641,928 (GRCm39)	missense	probably damaging	1.00
R5810:Vps13a	UTSW	19	16,643,688 (GRCm39)	missense	probably benign	0.00
R5866:Vps13a	UTSW	19	16,657,387 (GRCm39)	missense	probably benign	0.04
R5886:Vps13a	UTSW	19	16,641,926 (GRCm39)	missense	probably benign	0.01
R5933:Vps13a	UTSW	19	16,637,894 (GRCm39)	missense	probably benign	0.34
R5965:Vps13a	UTSW	19	16,596,392 (GRCm39)	splice site	probably null
R6259:Vps13a	UTSW	19	16,664,534 (GRCm39)	nonsense	probably null
R6346:Vps13a	UTSW	19	16,659,578 (GRCm39)	missense	possibly damaging	0.94
R6459:Vps13a	UTSW	19	16,641,382 (GRCm39)	missense	possibly damaging	0.56
R6485:Vps13a	UTSW	19	16,657,414 (GRCm39)	missense	probably damaging	0.99
R6520:Vps13a	UTSW	19	16,702,943 (GRCm39)	missense	probably damaging	1.00
R6644:Vps13a	UTSW	19	16,722,283 (GRCm39)	missense	possibly damaging	0.90
R6932:Vps13a	UTSW	19	16,655,439 (GRCm39)	missense	probably benign	0.01
R6934:Vps13a	UTSW	19	16,653,558 (GRCm39)	missense	probably damaging	1.00
R6951:Vps13a	UTSW	19	16,701,104 (GRCm39)	missense	probably benign	0.00
R7027:Vps13a	UTSW	19	16,642,028 (GRCm39)	missense	probably benign	0.01
R7126:Vps13a	UTSW	19	16,688,243 (GRCm39)	missense	probably benign
R7206:Vps13a	UTSW	19	16,731,662 (GRCm39)	missense	probably damaging	1.00
R7248:Vps13a	UTSW	19	16,655,406 (GRCm39)	missense	probably benign	0.25
R7252:Vps13a	UTSW	19	16,638,428 (GRCm39)	missense	probably benign	0.00
R7255:Vps13a	UTSW	19	16,631,703 (GRCm39)	critical splice donor site	probably null
R7382:Vps13a	UTSW	19	16,596,849 (GRCm39)	missense	probably damaging	1.00
R7422:Vps13a	UTSW	19	16,727,537 (GRCm39)	missense	probably damaging	1.00
R7425:Vps13a	UTSW	19	16,701,066 (GRCm39)	missense	probably benign	0.13
R7523:Vps13a	UTSW	19	16,681,153 (GRCm39)	missense	probably benign
R7586:Vps13a	UTSW	19	16,624,962 (GRCm39)	missense	probably benign	0.08
R7587:Vps13a	UTSW	19	16,681,153 (GRCm39)	missense	probably benign	0.00
R7593:Vps13a	UTSW	19	16,703,027 (GRCm39)	missense	probably damaging	1.00
R7637:Vps13a	UTSW	19	16,727,513 (GRCm39)	missense	probably benign	0.02
R7763:Vps13a	UTSW	19	16,723,364 (GRCm39)	missense	possibly damaging	0.95
R7813:Vps13a	UTSW	19	16,628,820 (GRCm39)	missense	possibly damaging	0.81
R7815:Vps13a	UTSW	19	16,702,936 (GRCm39)	missense	probably damaging	1.00
R7861:Vps13a	UTSW	19	16,632,668 (GRCm39)	missense	probably damaging	1.00
R7909:Vps13a	UTSW	19	16,697,794 (GRCm39)	nonsense	probably null
R7939:Vps13a	UTSW	19	16,718,155 (GRCm39)	missense	possibly damaging	0.94
R8108:Vps13a	UTSW	19	16,618,151 (GRCm39)	missense	probably damaging	1.00
R8123:Vps13a	UTSW	19	16,625,066 (GRCm39)	missense	probably benign	0.01
R8134:Vps13a	UTSW	19	16,631,718 (GRCm39)	missense	possibly damaging	0.71
R8168:Vps13a	UTSW	19	16,726,912 (GRCm39)	missense	probably benign	0.09
R8272:Vps13a	UTSW	19	16,727,209 (GRCm39)	critical splice donor site	probably null
R8293:Vps13a	UTSW	19	16,645,969 (GRCm39)	missense	possibly damaging	0.81
R8303:Vps13a	UTSW	19	16,594,270 (GRCm39)	missense	probably benign	0.00
R8383:Vps13a	UTSW	19	16,701,069 (GRCm39)	missense	possibly damaging	0.83
R8386:Vps13a	UTSW	19	16,678,483 (GRCm39)	critical splice donor site	probably null
R8433:Vps13a	UTSW	19	16,718,600 (GRCm39)	missense	possibly damaging	0.56
R8436:Vps13a	UTSW	19	16,718,157 (GRCm39)	missense	probably benign	0.10
R8450:Vps13a	UTSW	19	16,631,871 (GRCm39)	splice site	probably null
R8476:Vps13a	UTSW	19	16,699,821 (GRCm39)	missense	possibly damaging	0.60
R8501:Vps13a	UTSW	19	16,659,484 (GRCm39)	missense	probably benign	0.39
R8552:Vps13a	UTSW	19	16,731,684 (GRCm39)	missense	probably damaging	0.99
R8680:Vps13a	UTSW	19	16,623,270 (GRCm39)	missense	possibly damaging	0.84
R8784:Vps13a	UTSW	19	16,642,153 (GRCm39)	missense	probably damaging	1.00
R8871:Vps13a	UTSW	19	16,641,186 (GRCm39)	missense	probably damaging	1.00
R8945:Vps13a	UTSW	19	16,642,114 (GRCm39)	missense	probably damaging	1.00
R8948:Vps13a	UTSW	19	16,723,340 (GRCm39)	missense	probably damaging	0.99
R8950:Vps13a	UTSW	19	16,723,340 (GRCm39)	missense	probably damaging	0.99
R8960:Vps13a	UTSW	19	16,683,247 (GRCm39)	missense	possibly damaging	0.67
R9189:Vps13a	UTSW	19	16,663,961 (GRCm39)	missense	probably benign
R9366:Vps13a	UTSW	19	16,672,894 (GRCm39)	missense	probably damaging	1.00
R9505:Vps13a	UTSW	19	16,719,908 (GRCm39)	missense	possibly damaging	0.94
R9601:Vps13a	UTSW	19	16,623,337 (GRCm39)	missense	possibly damaging	0.84
R9735:Vps13a	UTSW	19	16,701,111 (GRCm39)	missense	probably damaging	1.00
R9776:Vps13a	UTSW	19	16,736,958 (GRCm39)	missense	probably benign
R9796:Vps13a	UTSW	19	16,631,828 (GRCm39)	missense	probably benign	0.01
X0061:Vps13a	UTSW	19	16,623,232 (GRCm39)	missense	probably benign	0.40
X0066:Vps13a	UTSW	19	16,719,917 (GRCm39)	missense	probably benign	0.33
Z1177:Vps13a	UTSW	19	16,676,477 (GRCm39)	critical splice acceptor site	probably null
Z31818:Vps13a	UTSW	19	16,758,118 (GRCm39)	missense	possibly damaging	0.94

Posted On

2015-04-16