Mutagenetix > Incidental Mutation

Incidental Mutation 'R0866:Gapvd1'

82332

Institutional Source

Beutler Lab

Gene Symbol

Gapvd1

Ensembl Gene

ENSMUSG00000026867

Gene Name

GTPase activating protein and VPS9 domains 1

Synonyms

2010005B09Rik, 4432404J10Rik

MMRRC Submission

039040-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0866 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

34566190-34645297 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 34599229 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Serine at position 669 (C669S)

Ref Sequence

ENSEMBL: ENSMUSP00000099864 (fasta)

Gene Model

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

AlphaFold

Q6PAR5

Predicted Effect

probably damaging
Transcript: ENSMUST00000028224
AA Change: C669S

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000028224
Gene: ENSMUSG00000026867
AA Change: C669S

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 damaging
Transcript: ENSMUST00000102800
AA Change: C669S

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000099864
Gene: ENSMUSG00000026867
AA Change: C669S

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 damaging
Transcript: ENSMUST00000113099
AA Change: C690S

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000108723
Gene: ENSMUSG00000026867
AA Change: C690S

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: ENSMUST00000113101

SMART Domains

Protein: ENSMUSP00000108725
Gene: ENSMUSG00000026867

Domain	Start	End	E-Value	Type
low complexity region	13	28	N/A	INTRINSIC
low complexity region	47	58	N/A	INTRINSIC
low complexity region	61	71	N/A	INTRINSIC
low complexity region	74	90	N/A	INTRINSIC
VPS9	443	548	1.08e-24	SMART

Predicted Effect

unknown
Transcript: ENSMUST00000113103
AA Change: C526S

SMART Domains

Protein: ENSMUSP00000108727
Gene: ENSMUSG00000026867
AA Change: C526S

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

unknown
Transcript: ENSMUST00000113111
AA Change: C127S

SMART Domains

Protein: ENSMUSP00000108735
Gene: ENSMUSG00000026867
AA Change: C127S

Domain	Start	End	E-Value	Type
internal_repeat_1	85	114	3.65e-6	PROSPERO
low complexity region	123	137	N/A	INTRINSIC
internal_repeat_1	145	176	3.65e-6	PROSPERO
low complexity region	334	349	N/A	INTRINSIC
low complexity region	368	379	N/A	INTRINSIC
low complexity region	382	392	N/A	INTRINSIC
low complexity region	395	411	N/A	INTRINSIC
low complexity region	431	441	N/A	INTRINSIC
VPS9	791	896	1.08e-24	SMART

Predicted Effect

unknown
Transcript: ENSMUST00000128855
AA Change: C30S

SMART Domains

Protein: ENSMUSP00000129138
Gene: ENSMUSG00000026867
AA Change: C30S

Domain	Start	End	E-Value	Type
low complexity region	26	40	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000137528
AA Change: C552S

SMART Domains

Protein: ENSMUSP00000120138
Gene: ENSMUSG00000026867
AA Change: C552S

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

noncoding transcript
Transcript: ENSMUST00000156098

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150859

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000167251

Meta Mutation Damage Score

0.3799

Coding Region Coverage

1x: 99.4%
3x: 98.6%
10x: 96.5%
20x: 91.7%

Validation Efficiency

100% (44/44)

Allele List at MGI

Other mutations in this stock

Total: 40 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5430401F13Rik	G	T	6: 131,529,742 (GRCm39)	R112L	unknown	Het
Abcd4	G	T	12: 84,658,507 (GRCm39)	A232E	probably damaging	Het
Acsm5	T	A	7: 119,140,123 (GRCm39)	I508N	probably damaging	Het
Adam22	T	C	5: 8,132,156 (GRCm39)	Q263R	probably damaging	Het
Ccdc88c	A	G	12: 100,879,451 (GRCm39)	L1890P	probably benign	Het
Ckap4	C	T	10: 84,363,384 (GRCm39)	D560N	probably damaging	Het
Crb3	T	A	17: 57,369,743 (GRCm39)	L17Q	probably damaging	Het
Fbxo21	G	T	5: 118,115,098 (GRCm39)	R78L	probably benign	Het
Gria2	A	T	3: 80,629,331 (GRCm39)		probably benign	Het
H2-M11	T	C	17: 36,859,829 (GRCm39)	L274P	probably benign	Het
Hmox1	A	G	8: 75,823,931 (GRCm39)	T200A	probably benign	Het
Hspa8	G	A	9: 40,713,920 (GRCm39)		probably null	Het
Isy1	C	A	6: 87,796,094 (GRCm39)	R281L	probably benign	Het
Kiz	C	A	2: 146,697,973 (GRCm39)		probably benign	Het
Lrig2	T	C	3: 104,371,591 (GRCm39)	K704R	probably benign	Het
Lrp1	A	T	10: 127,375,147 (GRCm39)	D4484E	probably damaging	Het
Lrrc7	C	A	3: 157,869,903 (GRCm39)		probably benign	Het
Mtmr14	T	C	6: 113,216,543 (GRCm39)		probably null	Het
Mtmr3	A	T	11: 4,438,474 (GRCm39)	V660E	probably benign	Het
Mtor	T	C	4: 148,570,513 (GRCm39)	I1190T	probably benign	Het
Mtrf1l	T	C	10: 5,763,376 (GRCm39)	R318G	probably damaging	Het
Myh7	T	C	14: 55,210,596 (GRCm39)	T1739A	probably benign	Het
Ofcc1	C	T	13: 40,362,305 (GRCm39)	G206R	probably benign	Het
Or5h18	C	T	16: 58,847,791 (GRCm39)	V160I	probably benign	Het
Pcca	A	G	14: 123,126,957 (GRCm39)	E722G	possibly damaging	Het
Pds5b	T	A	5: 150,662,656 (GRCm39)		probably benign	Het
Ralgapa2	A	T	2: 146,277,923 (GRCm39)	F413I	probably damaging	Het
Rbbp9	T	C	2: 144,392,628 (GRCm39)	Y24C	probably damaging	Het
Rgs2	A	G	1: 143,877,988 (GRCm39)	S103P	probably damaging	Het
Rtn1	G	T	12: 72,355,156 (GRCm39)	Y263*	probably null	Het
Slc22a1	T	C	17: 12,875,933 (GRCm39)	E427G	probably benign	Het
Speg	A	G	1: 75,393,727 (GRCm39)	T1695A	probably damaging	Het
Tlx3	C	A	11: 33,153,315 (GRCm39)	G49W	probably damaging	Het
Tor1b	A	G	2: 30,846,928 (GRCm39)	M292V	probably benign	Het
Tspyl3	A	T	2: 153,066,854 (GRCm39)	L128Q	probably damaging	Het
Zbtb14	C	A	17: 69,695,497 (GRCm39)	F398L	probably damaging	Het
Zfc3h1	G	A	10: 115,263,621 (GRCm39)	V1821I	probably benign	Het
Zfhx4	A	T	3: 5,477,272 (GRCm39)	T3271S	possibly damaging	Het
Zfp386	G	T	12: 116,018,329 (GRCm39)		probably benign	Het
Zfp574	A	T	7: 24,779,323 (GRCm39)	K115M	probably damaging	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
R0840:Gapvd1	UTSW	2	34,619,125 (GRCm39)	missense	probably benign	0.29
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'- TGTTCTAGTgggctggagagatgg -3'
(R):5'- TGTCCCCAACTGGGAACTTTGTG -3'

Sequencing Primer
(F):5'- aggtgctgaggtaaatgtctg -3'
(R):5'- AACTTTGTGTTTTTAGTTTCGTGC -3'

Posted On

2013-11-08