Mutagenetix > Incidental Mutation

Incidental Mutation 'R9066:Gapvd1'

689249

Institutional Source

Beutler Lab

Gene Symbol

Gapvd1

Ensembl Gene

ENSMUSG00000026867

Gene Name

GTPase activating protein and VPS9 domains 1

Synonyms

2010005B09Rik, 4432404J10Rik

MMRRC Submission

068891-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9066 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

34566190-34645297 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 34617297 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Histidine at position 349 (Q349H)

Ref Sequence

ENSEMBL: ENSMUSP00000099864 (fasta)

Gene Model

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

AlphaFold

Q6PAR5

Predicted Effect

probably damaging
Transcript: ENSMUST00000028224
AA Change: Q349H

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000028224
Gene: ENSMUSG00000026867
AA Change: Q349H

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: Q349H

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000099864
Gene: ENSMUSG00000026867
AA Change: Q349H

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: Q349H

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

SMART Domains

Protein: ENSMUSP00000108723
Gene: ENSMUSG00000026867
AA Change: Q349H

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: Q179H

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: ENSMUSP00000120138
Gene: ENSMUSG00000026867
AA Change: Q211H

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

SMART Domains

Protein: ENSMUSP00000126225
Gene: ENSMUSG00000026867

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

Validation Efficiency

96% (46/48)

Allele List at MGI

Other mutations in this stock

Total: 48 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca7	A	G	10: 79,849,188 (GRCm39)	T1858A	probably damaging	Het
Atp1a1	A	G	3: 101,489,338 (GRCm39)	I758T	probably damaging	Het
Atp2c1	T	C	9: 105,330,845 (GRCm39)	E225G	probably damaging	Het
Clec7a	A	C	6: 129,444,491 (GRCm39)	S115A	probably benign	Het
Cnbd1	T	C	4: 19,098,181 (GRCm39)	T80A	probably benign	Het
Ctu1	A	G	7: 43,326,019 (GRCm39)	H226R	possibly damaging	Het
Dctn4	T	C	18: 60,659,387 (GRCm39)	F29L	probably damaging	Het
Dnajb2	A	G	1: 75,217,874 (GRCm39)	T169A		Het
Efcab3	T	A	11: 104,631,688 (GRCm39)		probably benign	Het
Esf1	A	T	2: 139,990,693 (GRCm39)	M597K	probably benign	Het
Fzd7	C	T	1: 59,521,991 (GRCm39)		probably benign	Het
Garin5b	T	C	7: 4,773,518 (GRCm39)		probably benign	Het
Gata5	A	G	2: 179,968,761 (GRCm39)	F371S		Het
Gm572	A	T	4: 148,751,278 (GRCm39)	Q217L	possibly damaging	Het
Igkv14-130	T	A	6: 67,768,219 (GRCm39)	M26K	probably damaging	Het
Jchain	T	G	5: 88,675,638 (GRCm39)	M1L	probably benign	Het
Kcnj14	G	A	7: 45,469,073 (GRCm39)	T144M	probably damaging	Het
Kirrel2	C	A	7: 30,153,454 (GRCm39)	A302S	probably damaging	Het
Klhl29	C	T	12: 5,260,114 (GRCm39)	V35I	probably benign	Het
Kndc1	C	T	7: 139,507,708 (GRCm39)	S1222F	possibly damaging	Het
Lgi4	A	C	7: 30,759,446 (GRCm39)	M1L	probably benign	Het
Ncr1	A	G	7: 4,347,552 (GRCm39)	D276G	probably benign	Het
Nfatc3	T	A	8: 106,825,782 (GRCm39)	M619K	probably benign	Het
Nudcd1	A	T	15: 44,243,588 (GRCm39)	F441I	probably damaging	Het
Nxt2	C	T	X: 141,020,747 (GRCm39)	A118V	possibly damaging	Het
Or10a3n	A	T	7: 108,493,253 (GRCm39)	Y125*	probably null	Het
Or8b12	T	G	9: 37,657,871 (GRCm39)	V147G	possibly damaging	Het
Pop1	A	T	15: 34,516,060 (GRCm39)	Q586L	possibly damaging	Het
Prss3b	C	T	6: 41,008,640 (GRCm39)	G225R	probably benign	Het
Rcbtb1	T	G	14: 59,462,206 (GRCm39)	I279S	possibly damaging	Het
Rsf1	CGGCGGCGG	CGGCGGCGGGGGCGGCGG	7: 97,229,118 (GRCm39)		probably benign	Het
Serpine3	A	G	14: 62,929,555 (GRCm39)	D401G	probably damaging	Het
Slc25a4	A	G	8: 46,662,115 (GRCm39)	V181A	probably damaging	Het
Slc26a2	T	G	18: 61,335,130 (GRCm39)	I108L	probably benign	Het
Slc27a5	A	C	7: 12,722,530 (GRCm39)	V648G	possibly damaging	Het
Slc2a7	T	C	4: 150,250,872 (GRCm39)	F431S	probably damaging	Het
Sox11	T	C	12: 27,391,422 (GRCm39)	H329R	possibly damaging	Het
Speg	G	A	1: 75,361,654 (GRCm39)	G223R	probably damaging	Het
Synpo2	G	A	3: 122,911,133 (GRCm39)	H171Y	possibly damaging	Het
Tle6	G	T	10: 81,430,212 (GRCm39)	N323K	possibly damaging	Het
Ugt3a1	A	T	15: 9,367,384 (GRCm39)	M376L	possibly damaging	Het
Unc13d	T	C	11: 115,957,561 (GRCm39)	K798R	probably benign	Het
Vasp	A	T	7: 18,998,433 (GRCm39)	H80Q	probably damaging	Het
Vmn2r28	T	C	7: 5,491,596 (GRCm39)	D217G	probably damaging	Het
Vps41	T	C	13: 19,008,018 (GRCm39)	S284P	probably damaging	Het
Zer1	A	C	2: 30,000,686 (GRCm39)	L245R	probably damaging	Het
Zfp516	G	T	18: 82,973,964 (GRCm39)	R54L	probably damaging	Het
Zfp868	T	C	8: 70,064,292 (GRCm39)	K348E	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
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'- ATGCAGAGTAAAAGTTGTGCACC -3'
(R):5'- GAATTACAGCAACGCTTTCTACTTC -3'

Sequencing Primer
(F):5'- GAGGACTCACTGTTATCTAGGCTAAC -3'
(R):5'- AGCTGACAGAGACAAGATACAC -3'

Posted On

2021-11-19