Mutagenetix > Incidental Mutation

Incidental Mutation 'R9470:Gapvd1'

715399

Institutional Source

Beutler Lab

Gene Symbol

Gapvd1

Ensembl Gene

ENSMUSG00000026867

Gene Name

GTPase activating protein and VPS9 domains 1

Synonyms

2010005B09Rik, 4432404J10Rik

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9470 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

34566190-34645297 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 34602280 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 622 (D622E)

Ref Sequence

ENSEMBL: ENSMUSP00000099864 (fasta)

Gene Model

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

AlphaFold

Q6PAR5

Predicted Effect

possibly damaging
Transcript: ENSMUST00000028224
AA Change: D622E

PolyPhen 2 Score 0.777 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000028224
Gene: ENSMUSG00000026867
AA Change: D622E

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

possibly damaging
Transcript: ENSMUST00000102800
AA Change: D622E

PolyPhen 2 Score 0.777 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000099864
Gene: ENSMUSG00000026867
AA Change: D622E

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

possibly damaging
Transcript: ENSMUST00000113099
AA Change: D643E

PolyPhen 2 Score 0.668 (Sensitivity: 0.86; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000108723
Gene: ENSMUSG00000026867
AA Change: D643E

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

SMART Domains

Protein: ENSMUSP00000108727
Gene: ENSMUSG00000026867
AA Change: D479E

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

SMART Domains

Protein: ENSMUSP00000108735
Gene: ENSMUSG00000026867
AA Change: D80E

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

probably benign
Transcript: ENSMUST00000128855

SMART Domains

Protein: ENSMUSP00000129138
Gene: ENSMUSG00000026867

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

Predicted Effect

SMART Domains

Protein: ENSMUSP00000120138
Gene: ENSMUSG00000026867
AA Change: D505E

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.5%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 44 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrb2	T	A	4: 129,903,074 (GRCm39)	L558Q	probably damaging	Het
Apob	A	G	12: 8,039,219 (GRCm39)	D483G	possibly damaging	Het
Arid1a	T	C	4: 133,413,057 (GRCm39)	D994G	unknown	Het
Barx2	A	T	9: 31,770,044 (GRCm39)	Y161*	probably null	Het
Bmp7	G	T	2: 172,711,960 (GRCm39)	N421K	probably damaging	Het
Bod1l	A	T	5: 41,974,439 (GRCm39)	C2292S	probably damaging	Het
Ces1c	C	T	8: 93,830,746 (GRCm39)		probably null	Het
Clca3b	T	C	3: 144,543,456 (GRCm39)	T458A	probably damaging	Het
Cntnap5a	T	G	1: 116,374,344 (GRCm39)	V952G	probably damaging	Het
Cyp2c54	T	C	19: 40,060,888 (GRCm39)	E85G	probably damaging	Het
Dmxl1	A	G	18: 50,026,777 (GRCm39)	K1962E	possibly damaging	Het
Dnajc13	A	G	9: 104,107,919 (GRCm39)	V254A	probably benign	Het
Dysf	A	T	6: 84,090,352 (GRCm39)	I955F	possibly damaging	Het
Fam184b	A	G	5: 45,741,854 (GRCm39)	S126P	probably damaging	Het
Ggta1	T	C	2: 35,292,767 (GRCm39)	Y180C	probably damaging	Het
Gpr31b	A	G	17: 13,270,845 (GRCm39)	V108A	probably damaging	Het
Kcnu1	A	G	8: 26,409,660 (GRCm39)	Y861C	probably benign	Het
Mov10l1	T	C	15: 88,904,518 (GRCm39)	L799P	probably damaging	Het
Nkx1-1	G	A	5: 33,591,275 (GRCm39)	P16S	unknown	Het
Nos1	T	C	5: 118,064,560 (GRCm39)	L997P	probably damaging	Het
Noxred1	A	G	12: 87,269,829 (GRCm39)	Y301H	possibly damaging	Het
Nup50l	T	C	6: 96,142,474 (GRCm39)	H190R	possibly damaging	Het
Or11g1	T	C	14: 50,651,235 (GRCm39)	V78A	possibly damaging	Het
Or52j3	G	A	7: 102,836,270 (GRCm39)	R154H	probably benign	Het
Or5ak4	A	T	2: 85,161,673 (GRCm39)	S190T	probably damaging	Het
Or5b113	A	G	19: 13,342,115 (GRCm39)	N41S	probably damaging	Het
Or6b6	A	T	7: 106,571,461 (GRCm39)	I30N	probably benign	Het
Paqr7	T	C	4: 134,234,914 (GRCm39)	V257A	probably benign	Het
Parp8	A	T	13: 117,031,292 (GRCm39)	S473R	probably benign	Het
Pcdhb14	A	T	18: 37,581,076 (GRCm39)	T61S	probably benign	Het
Pde11a	G	A	2: 75,821,612 (GRCm39)	A889V	probably benign	Het
Potefam3e	T	A	8: 19,797,809 (GRCm39)	S292T	probably benign	Het
Scart2	A	G	7: 139,827,345 (GRCm39)	T18A	probably benign	Het
Sertad1	T	C	7: 27,188,871 (GRCm39)	L64P	probably damaging	Het
Tmem156	C	T	5: 65,237,531 (GRCm39)	R43K	probably damaging	Het
Tmem82	T	A	4: 141,342,341 (GRCm39)	D287V	probably damaging	Het
Traf1	A	G	2: 34,833,974 (GRCm39)	F381L	probably benign	Het
Trim44	T	C	2: 102,230,651 (GRCm39)	S127G	unknown	Het
Tyw1	G	A	5: 130,298,065 (GRCm39)	R202Q	probably damaging	Het
Ubap2	G	A	4: 41,195,434 (GRCm39)	A1068V	possibly damaging	Het
Vmn1r47	T	G	6: 89,999,777 (GRCm39)	M303R	probably null	Het
Zc3h12d	T	C	10: 7,743,321 (GRCm39)	S364P	possibly damaging	Het
Zdbf2	T	A	1: 63,344,784 (GRCm39)	N1054K	possibly damaging	Het
Zpbp	A	T	11: 11,358,541 (GRCm39)	I242N	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
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
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'- ATACCAGCTTCCCAGGCTAGAG -3'
(R):5'- TTAATTAGTCAGTGGGGAGCAG -3'

Sequencing Primer
(F):5'- TAGAGCCACCCACTCCCATG -3'
(R):5'- AGGCTGGAACTACGTGCTTATTAATG -3'

Posted On

2022-06-15