Mutagenetix > Incidental Mutation

Incidental Mutation 'R7742:Gapvd1'

596588

Institutional Source

Beutler Lab

Gene Symbol

Gapvd1

Ensembl Gene

ENSMUSG00000026867

Gene Name

GTPase activating protein and VPS9 domains 1

Synonyms

2010005B09Rik, 4432404J10Rik

MMRRC Submission

045798-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7742 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

34566190-34645297 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 34568635 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 1328 (L1328P)

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: L1328P

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000028224
Gene: ENSMUSG00000026867
AA Change: L1328P

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: L1328P

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000099864
Gene: ENSMUSG00000026867
AA Change: L1328P

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: L1349P

PolyPhen 2 Score 0.504 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000108723
Gene: ENSMUSG00000026867
AA Change: L1349P

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: ENSMUSP00000108725
Gene: ENSMUSG00000026867
AA Change: L438P

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

SMART Domains

Protein: ENSMUSP00000108735
Gene: ENSMUSG00000026867
AA Change: L786P

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: ENSMUST00000138203

Meta Mutation Damage Score

0.7107

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.2%

Validation Efficiency

100% (53/53)

Allele List at MGI

Other mutations in this stock

Total: 53 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3425401B19Rik	T	C	14: 32,384,714 (GRCm39)	K417R	possibly damaging	Het
Adgrl2	A	T	3: 148,542,064 (GRCm39)	I886N	probably damaging	Het
Angptl2	A	G	2: 33,133,928 (GRCm39)	T417A	probably damaging	Het
Ankrd33b	T	C	15: 31,367,538 (GRCm39)	M1V	probably null	Het
Col3a1	A	G	1: 45,384,161 (GRCm39)	H1155R	unknown	Het
Csad	A	G	15: 102,095,599 (GRCm39)	S153P	probably damaging	Het
Dennd1b	G	A	1: 138,990,611 (GRCm39)	E192K	probably damaging	Het
Dmtf1	C	T	5: 9,172,457 (GRCm39)		probably benign	Het
Dna2	T	C	10: 62,809,073 (GRCm39)	I1055T	probably benign	Het
Dnai4	C	T	4: 102,947,630 (GRCm39)	M215I	probably benign	Het
Dync2h1	T	C	9: 7,076,232 (GRCm39)	D2975G	probably benign	Het
Eif1ad7	A	T	12: 88,238,476 (GRCm39)	Y95N	probably damaging	Het
F5	G	T	1: 164,035,453 (GRCm39)	V1876F	possibly damaging	Het
Fam81b	T	A	13: 76,399,809 (GRCm39)	I150F	probably damaging	Het
Fbl	T	A	7: 27,877,684 (GRCm39)	V252E	probably damaging	Het
Fbln1	A	G	15: 85,124,917 (GRCm39)	D475G	probably damaging	Het
Fshr	T	A	17: 89,293,590 (GRCm39)	I363F	probably benign	Het
Hcfc2	T	A	10: 82,547,659 (GRCm39)		probably null	Het
Ifi209	C	A	1: 173,470,198 (GRCm39)	T262K	probably damaging	Het
Kif2b	T	A	11: 91,467,411 (GRCm39)	I291F	possibly damaging	Het
Lrp1b	T	A	2: 40,712,641 (GRCm39)	D3231V		Het
Mcidas	G	A	13: 113,135,521 (GRCm39)	G315S	probably damaging	Het
Naip5	T	A	13: 100,356,338 (GRCm39)	E1092D	probably benign	Het
Nudcd1	T	C	15: 44,268,754 (GRCm39)	K209E	probably benign	Het
Nup98	C	T	7: 101,802,464 (GRCm39)		probably null	Het
Odad3	T	C	9: 21,904,193 (GRCm39)	D361G	possibly damaging	Het
Or2ag2	T	C	7: 106,485,829 (GRCm39)	Q65R	probably damaging	Het
Or2j6	T	A	7: 139,980,234 (GRCm39)	I242F	probably benign	Het
Pign	T	C	1: 105,480,122 (GRCm39)	I851V	probably benign	Het
Pkd1l3	T	A	8: 110,341,204 (GRCm39)	L19Q	unknown	Het
Plat	G	T	8: 23,262,248 (GRCm39)	G91W	probably damaging	Het
Plekhm2	A	G	4: 141,355,150 (GRCm39)	L959P	probably benign	Het
Prkcg	T	C	7: 3,378,459 (GRCm39)	I627T	possibly damaging	Het
Prl7b1	A	T	13: 27,791,031 (GRCm39)	M18K	probably benign	Het
Ptpn3	T	A	4: 57,265,092 (GRCm39)		probably null	Het
Rp1	A	T	1: 4,240,457 (GRCm39)	F899I	unknown	Het
Sis	T	A	3: 72,832,431 (GRCm39)	Y1026F	probably benign	Het
Slc4a10	T	G	2: 62,127,194 (GRCm39)	V879G	probably damaging	Het
Specc1l	T	C	10: 75,082,251 (GRCm39)	I549T	probably benign	Het
Spmip11	T	A	15: 98,483,250 (GRCm39)	V60E	probably damaging	Het
Sprr2a3	G	A	3: 92,196,066 (GRCm39)	V58M	unknown	Het
Sptbn2	C	G	19: 4,799,040 (GRCm39)	R2037G	probably benign	Het
Syne2	C	T	12: 76,106,209 (GRCm39)	H785Y	probably benign	Het
Tat	T	A	8: 110,718,242 (GRCm39)	N42K	probably benign	Het
Tmem184a	C	T	5: 139,792,744 (GRCm39)	A271T	probably benign	Het
Tmprss11d	T	C	5: 86,451,493 (GRCm39)	I411V	probably damaging	Het
Ttn	T	C	2: 76,733,872 (GRCm39)	I4468V	unknown	Het
Vcam1	T	C	3: 115,909,734 (GRCm39)	N531S	possibly damaging	Het
Vmn1r257	C	T	7: 22,391,343 (GRCm39)	V134I	probably benign	Het
Xcl1	T	C	1: 164,763,041 (GRCm39)	T7A	unknown	Het
Zc3h11a	A	G	1: 133,565,173 (GRCm39)	V242A	probably benign	Het
Zc3h7a	A	T	16: 10,971,025 (GRCm39)	Y335N	probably benign	Het
Zp2	T	C	7: 119,731,731 (GRCm39)	I675V	unknown	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
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'- AGGAACAAAGTCATCTGCCC -3'
(R):5'- GGAAAATCTCATCCCAGCTTTG -3'

Sequencing Primer
(F):5'- AAAGTCATCTGCCCCGGGG -3'
(R):5'- CCAGGCTCTGTGGTATATATACAC -3'

Posted On

2019-11-26