Mutagenetix > Incidental Mutation

Incidental Mutation 'R0840:Gapvd1'

77097

Institutional Source

Beutler Lab

Gene Symbol

Gapvd1

Ensembl Gene

ENSMUSG00000026867

Gene Name

GTPase activating protein and VPS9 domains 1

Synonyms

2010005B09Rik, 4432404J10Rik

MMRRC Submission

039019-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0840 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

34566190-34645297 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 34619125 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Phenylalanine at position 83 (V83F)

Ref Sequence

ENSEMBL: ENSMUSP00000126225 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000028224] [ENSMUST00000102800] [ENSMUST00000113099] [ENSMUST00000142436]

AlphaFold

Q6PAR5

Predicted Effect

probably benign
Transcript: ENSMUST00000028224
AA Change: V83F

PolyPhen 2 Score 0.221 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000028224
Gene: ENSMUSG00000026867
AA Change: V83F

Domain	Start	End	E-Value	Type
Pfam:RasGAP	152	353	2.3e-36	PFAM
internal_repeat_1	626	655	3.27e-5	PROSPERO
low complexity region	664	678	N/A	INTRINSIC
internal_repeat_1	686	717	3.27e-5	PROSPERO
low complexity region	875	890	N/A	INTRINSIC
low complexity region	909	920	N/A	INTRINSIC
low complexity region	923	933	N/A	INTRINSIC
low complexity region	936	952	N/A	INTRINSIC
low complexity region	972	982	N/A	INTRINSIC
VPS9	1332	1437	1.08e-24	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000102800
AA Change: V83F

PolyPhen 2 Score 0.221 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000099864
Gene: ENSMUSG00000026867
AA Change: V83F

Domain	Start	End	E-Value	Type
Pfam:RasGAP	152	353	2.3e-36	PFAM
internal_repeat_1	626	655	3.27e-5	PROSPERO
low complexity region	664	678	N/A	INTRINSIC
internal_repeat_1	686	717	3.27e-5	PROSPERO
low complexity region	875	890	N/A	INTRINSIC
low complexity region	909	920	N/A	INTRINSIC
low complexity region	923	933	N/A	INTRINSIC
low complexity region	936	952	N/A	INTRINSIC
low complexity region	972	982	N/A	INTRINSIC
VPS9	1332	1437	1.08e-24	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000113099
AA Change: V83F

PolyPhen 2 Score 0.221 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000108723
Gene: ENSMUSG00000026867
AA Change: V83F

Domain	Start	End	E-Value	Type
Pfam:RasGAP	152	353	2.8e-37	PFAM
internal_repeat_1	647	676	3.6e-5	PROSPERO
low complexity region	685	699	N/A	INTRINSIC
internal_repeat_1	707	738	3.6e-5	PROSPERO
low complexity region	896	911	N/A	INTRINSIC
low complexity region	930	941	N/A	INTRINSIC
low complexity region	944	954	N/A	INTRINSIC
low complexity region	957	973	N/A	INTRINSIC
low complexity region	993	1003	N/A	INTRINSIC
VPS9	1353	1458	1.08e-24	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000113103

SMART Domains

Protein: ENSMUSP00000108727
Gene: ENSMUSG00000026867

Domain	Start	End	E-Value	Type
Pfam:RasGAP	1	184	4.9e-32	PFAM
internal_repeat_1	484	513	1.18e-5	PROSPERO
low complexity region	522	536	N/A	INTRINSIC
internal_repeat_1	544	575	1.18e-5	PROSPERO
low complexity region	733	748	N/A	INTRINSIC
low complexity region	767	778	N/A	INTRINSIC
low complexity region	781	791	N/A	INTRINSIC
low complexity region	794	810	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000137528

SMART Domains

Protein: ENSMUSP00000120138
Gene: ENSMUSG00000026867

Domain	Start	End	E-Value	Type
Pfam:RasGAP	15	216	1.2e-37	PFAM
internal_repeat_1	510	539	1.19e-5	PROSPERO
low complexity region	548	562	N/A	INTRINSIC
internal_repeat_1	570	601	1.19e-5	PROSPERO
low complexity region	733	748	N/A	INTRINSIC
low complexity region	767	778	N/A	INTRINSIC
low complexity region	781	791	N/A	INTRINSIC
low complexity region	794	810	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000142436
AA Change: V83F

PolyPhen 2 Score 0.290 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000126225
Gene: ENSMUSG00000026867
AA Change: V83F

Domain	Start	End	E-Value	Type
SCOP:d1wer__	95	135	6e-4	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000169207

Meta Mutation Damage Score

0.1231

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.1%
20x: 94.1%

Validation Efficiency

100% (51/51)

Allele List at MGI

Other mutations in this stock

Total: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2700049A03Rik	C	G	12: 71,205,657 (GRCm39)	Q434E	probably benign	Het
A930011G23Rik	T	C	5: 99,382,547 (GRCm39)	T234A	probably benign	Het
Acot5	G	A	12: 84,122,614 (GRCm39)	W399*	probably null	Het
Adra1a	A	G	14: 66,965,159 (GRCm39)	E383G	possibly damaging	Het
Ahnak	T	A	19: 8,982,427 (GRCm39)	I1237N	probably damaging	Het
Bsg	A	G	10: 79,545,519 (GRCm39)	T28A	probably damaging	Het
Cacna1i	A	T	15: 80,243,150 (GRCm39)	I436F	possibly damaging	Het
Cd109	T	C	9: 78,571,612 (GRCm39)	I417T	probably benign	Het
Cep295	A	T	9: 15,245,611 (GRCm39)	D948E	probably benign	Het
Cfap92	G	T	6: 87,657,260 (GRCm39)		noncoding transcript	Het
Clcn3	C	A	8: 61,382,188 (GRCm39)	V467F	probably benign	Het
Cntnap3	T	C	13: 64,935,724 (GRCm39)	S380G	possibly damaging	Het
Dab1	C	T	4: 104,588,948 (GRCm39)	A524V	probably benign	Het
Dll4	T	A	2: 119,156,966 (GRCm39)	N79K	probably benign	Het
Ep300	A	T	15: 81,529,134 (GRCm39)	N1558I	unknown	Het
Fblim1	A	G	4: 141,308,320 (GRCm39)	F330L	possibly damaging	Het
Fbxo46	T	A	7: 18,871,073 (GRCm39)	M564K	possibly damaging	Het
Fnip1	T	A	11: 54,384,007 (GRCm39)		probably benign	Het
Foxl2	A	T	9: 98,837,984 (GRCm39)	K91*	probably null	Het
Guk1	G	A	11: 59,075,921 (GRCm39)	R146C	probably damaging	Het
Irf8	G	A	8: 121,480,220 (GRCm39)	G153S	probably benign	Het
Kcnu1	T	A	8: 26,403,712 (GRCm39)	M1K	probably null	Het
Krt32	G	A	11: 99,972,068 (GRCm39)	P427S	probably benign	Het
Lrp12	A	G	15: 39,739,554 (GRCm39)	S529P	probably damaging	Het
Mettl22	T	C	16: 8,300,021 (GRCm39)	V134A	probably damaging	Het
Morc2b	G	T	17: 33,355,086 (GRCm39)	H895Q	probably benign	Het
Nrros	T	C	16: 31,962,241 (GRCm39)	D556G	probably damaging	Het
Nrxn3	A	G	12: 90,298,567 (GRCm39)	S1367G	possibly damaging	Het
Or10al7	A	G	17: 38,366,463 (GRCm39)	F7S	probably benign	Het
Or56b1b	A	T	7: 108,164,823 (GRCm39)	S60T	probably benign	Het
Pcnx3	T	A	19: 5,735,729 (GRCm39)		probably null	Het
Pgap2	A	T	7: 101,886,655 (GRCm39)	M226L	probably damaging	Het
Pik3c2g	A	G	6: 139,841,798 (GRCm39)	I616M	probably damaging	Het
Pisd	A	G	5: 32,894,656 (GRCm39)	I380T	probably damaging	Het
Pkhd1	T	C	1: 20,420,745 (GRCm39)	I2454V	probably damaging	Het
Plpp2	A	G	10: 79,363,378 (GRCm39)	I151T	probably benign	Het
Polr3a	G	A	14: 24,502,268 (GRCm39)	T1295I	possibly damaging	Het
Pot1a	T	C	6: 25,748,283 (GRCm39)		probably benign	Het
Prpf39	T	G	12: 65,094,980 (GRCm39)	N219K	probably benign	Het
Rnf17	T	A	14: 56,712,904 (GRCm39)	N790K	probably damaging	Het
Slit3	C	T	11: 35,514,263 (GRCm39)		probably benign	Het
Stx1a	T	A	5: 135,070,088 (GRCm39)		probably benign	Het
Tenm3	C	A	8: 48,788,777 (GRCm39)	V690F	probably damaging	Het
Tmcc3	A	G	10: 94,414,633 (GRCm39)	I143V	probably benign	Het
Tmem41b	G	A	7: 109,580,256 (GRCm39)	S36F	probably damaging	Het
Trim5	A	T	7: 103,914,978 (GRCm39)	W364R	probably damaging	Het
Ttn	T	C	2: 76,617,155 (GRCm39)	Y16403C	probably damaging	Het
Vps8	T	C	16: 21,275,071 (GRCm39)	S210P	probably damaging	Het
Zbtb3	T	A	19: 8,780,821 (GRCm39)	S145T	possibly damaging	Het
Zfp882	T	A	8: 72,668,530 (GRCm39)	C452*	probably null	Het

Other mutations in Gapvd1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00799:Gapvd1	APN	2	34,589,872 (GRCm39)	missense	probably benign	0.00
IGL00985:Gapvd1	APN	2	34,585,575 (GRCm39)	missense	probably damaging	0.99
IGL01133:Gapvd1	APN	2	34,615,410 (GRCm39)	missense	probably damaging	0.98
IGL01347:Gapvd1	APN	2	34,596,708 (GRCm39)	critical splice donor site	probably null
IGL01830:Gapvd1	APN	2	34,578,968 (GRCm39)	missense	probably benign	0.44
IGL01865:Gapvd1	APN	2	34,585,515 (GRCm39)	missense	probably null
IGL02009:Gapvd1	APN	2	34,594,203 (GRCm39)	missense	probably damaging	1.00
IGL02014:Gapvd1	APN	2	34,594,203 (GRCm39)	missense	probably damaging	1.00
IGL02189:Gapvd1	APN	2	34,618,556 (GRCm39)	missense	probably damaging	1.00
IGL02418:Gapvd1	APN	2	34,620,530 (GRCm39)	missense	probably benign	0.00
IGL02632:Gapvd1	APN	2	34,574,186 (GRCm39)	splice site	probably benign
IGL02636:Gapvd1	APN	2	34,615,416 (GRCm39)	missense	probably benign	0.01
IGL02643:Gapvd1	APN	2	34,594,192 (GRCm39)	missense	probably damaging	1.00
IGL03271:Gapvd1	APN	2	34,617,219 (GRCm39)	unclassified	probably benign
P0023:Gapvd1	UTSW	2	34,596,700 (GRCm39)	splice site	probably benign
R0016:Gapvd1	UTSW	2	34,589,925 (GRCm39)	splice site	probably benign
R0016:Gapvd1	UTSW	2	34,589,925 (GRCm39)	splice site	probably benign
R0029:Gapvd1	UTSW	2	34,568,153 (GRCm39)	missense	probably damaging	1.00
R0029:Gapvd1	UTSW	2	34,568,153 (GRCm39)	missense	probably damaging	1.00
R0282:Gapvd1	UTSW	2	34,578,972 (GRCm39)	nonsense	probably null
R0414:Gapvd1	UTSW	2	34,583,439 (GRCm39)	missense	probably benign	0.14
R0443:Gapvd1	UTSW	2	34,594,633 (GRCm39)	intron	probably benign
R0542:Gapvd1	UTSW	2	34,615,048 (GRCm39)	unclassified	probably benign
R0570:Gapvd1	UTSW	2	34,618,552 (GRCm39)	missense	probably damaging	1.00
R0866:Gapvd1	UTSW	2	34,599,229 (GRCm39)	missense	probably damaging	1.00
R0890:Gapvd1	UTSW	2	34,602,329 (GRCm39)	missense	probably damaging	1.00
R0926:Gapvd1	UTSW	2	34,602,337 (GRCm39)	missense	probably damaging	1.00
R0970:Gapvd1	UTSW	2	34,620,625 (GRCm39)	splice site	probably null
R1168:Gapvd1	UTSW	2	34,594,481 (GRCm39)	missense	probably damaging	1.00
R1391:Gapvd1	UTSW	2	34,596,814 (GRCm39)	missense	probably damaging	1.00
R1577:Gapvd1	UTSW	2	34,599,240 (GRCm39)	missense	probably damaging	1.00
R1585:Gapvd1	UTSW	2	34,602,207 (GRCm39)	missense	possibly damaging	0.93
R1669:Gapvd1	UTSW	2	34,620,694 (GRCm39)	critical splice acceptor site	probably null
R1677:Gapvd1	UTSW	2	34,590,773 (GRCm39)	critical splice donor site	probably null
R1812:Gapvd1	UTSW	2	34,615,076 (GRCm39)	nonsense	probably null
R1874:Gapvd1	UTSW	2	34,596,033 (GRCm39)	missense	probably damaging	1.00
R1878:Gapvd1	UTSW	2	34,615,212 (GRCm39)	missense	probably benign	0.00
R1974:Gapvd1	UTSW	2	34,590,853 (GRCm39)	missense	probably damaging	0.99
R2111:Gapvd1	UTSW	2	34,574,329 (GRCm39)	missense	probably benign	0.08
R2921:Gapvd1	UTSW	2	34,578,875 (GRCm39)	missense	probably damaging	0.97
R2923:Gapvd1	UTSW	2	34,578,875 (GRCm39)	missense	probably damaging	0.97
R3846:Gapvd1	UTSW	2	34,619,084 (GRCm39)	nonsense	probably null
R3894:Gapvd1	UTSW	2	34,618,488 (GRCm39)	missense	probably benign	0.23
R4405:Gapvd1	UTSW	2	34,618,747 (GRCm39)	missense	probably damaging	1.00
R4605:Gapvd1	UTSW	2	34,618,549 (GRCm39)	missense	probably damaging	1.00
R4770:Gapvd1	UTSW	2	34,581,193 (GRCm39)	missense	probably damaging	0.98
R4935:Gapvd1	UTSW	2	34,594,504 (GRCm39)	nonsense	probably null
R5218:Gapvd1	UTSW	2	34,618,488 (GRCm39)	missense	probably benign	0.23
R5490:Gapvd1	UTSW	2	34,583,445 (GRCm39)	missense	probably benign	0.23
R5571:Gapvd1	UTSW	2	34,605,265 (GRCm39)	missense	probably damaging	1.00
R5588:Gapvd1	UTSW	2	34,599,166 (GRCm39)	missense	probably damaging	1.00
R5933:Gapvd1	UTSW	2	34,574,303 (GRCm39)	missense	probably benign	0.27
R6117:Gapvd1	UTSW	2	34,580,471 (GRCm39)	splice site	probably null
R6661:Gapvd1	UTSW	2	34,618,450 (GRCm39)	missense	probably damaging	1.00
R6857:Gapvd1	UTSW	2	34,618,389 (GRCm39)	missense	probably damaging	1.00
R6950:Gapvd1	UTSW	2	34,574,257 (GRCm39)	missense	probably benign	0.04
R7009:Gapvd1	UTSW	2	34,590,829 (GRCm39)	missense	probably damaging	1.00
R7125:Gapvd1	UTSW	2	34,585,612 (GRCm39)	missense	probably benign
R7154:Gapvd1	UTSW	2	34,615,075 (GRCm39)	missense	probably damaging	1.00
R7316:Gapvd1	UTSW	2	34,594,681 (GRCm39)	missense	probably damaging	1.00
R7358:Gapvd1	UTSW	2	34,580,473 (GRCm39)	critical splice donor site	probably null
R7363:Gapvd1	UTSW	2	34,602,207 (GRCm39)	missense	probably benign	0.01
R7371:Gapvd1	UTSW	2	34,607,385 (GRCm39)	missense	probably benign
R7418:Gapvd1	UTSW	2	34,615,130 (GRCm39)	missense	probably benign	0.12
R7690:Gapvd1	UTSW	2	34,619,134 (GRCm39)	missense	possibly damaging	0.68
R7740:Gapvd1	UTSW	2	34,590,834 (GRCm39)	missense	probably damaging	1.00
R7742:Gapvd1	UTSW	2	34,568,635 (GRCm39)	missense	probably damaging	1.00
R7857:Gapvd1	UTSW	2	34,619,079 (GRCm39)	missense	probably benign	0.06
R8062:Gapvd1	UTSW	2	34,568,126 (GRCm39)	missense	probably benign	0.37
R8113:Gapvd1	UTSW	2	34,594,330 (GRCm39)	missense	probably damaging	0.98
R8303:Gapvd1	UTSW	2	34,602,212 (GRCm39)	missense	probably damaging	1.00
R8558:Gapvd1	UTSW	2	34,594,493 (GRCm39)	missense	probably damaging	1.00
R8751:Gapvd1	UTSW	2	34,568,078 (GRCm39)	missense	probably damaging	0.96
R8781:Gapvd1	UTSW	2	34,610,698 (GRCm39)	missense	probably benign	0.37
R8794:Gapvd1	UTSW	2	34,594,330 (GRCm39)	missense	possibly damaging	0.49
R8876:Gapvd1	UTSW	2	34,568,560 (GRCm39)	missense	possibly damaging	0.95
R8942:Gapvd1	UTSW	2	34,619,134 (GRCm39)	missense	probably benign	0.06
R8954:Gapvd1	UTSW	2	34,568,110 (GRCm39)	missense	probably damaging	1.00
R9066:Gapvd1	UTSW	2	34,617,297 (GRCm39)	missense	probably damaging	1.00
R9428:Gapvd1	UTSW	2	34,607,318 (GRCm39)	missense	probably damaging	1.00
R9470:Gapvd1	UTSW	2	34,602,280 (GRCm39)	missense	possibly damaging	0.78
R9505:Gapvd1	UTSW	2	34,613,026 (GRCm39)	missense
R9690:Gapvd1	UTSW	2	34,618,492 (GRCm39)	missense	probably damaging	1.00
Z1177:Gapvd1	UTSW	2	34,589,876 (GRCm39)	missense	possibly damaging	0.78

Predicted Primers

PCR Primer
(F):5'- GGCTCATGCAAAGTAGCCGTAAGG -3'
(R):5'- TCAAGGAGATGTCACTGTTGGCAC -3'

Sequencing Primer
(F):5'- ACCTGAAGGAGGTAGCTTTCATC -3'
(R):5'- CACTGTTGGCACAGTAATGAACTC -3'

Posted On

2013-10-16