Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02636:Gapvd1'

301515

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Gapvd1

Ensembl Gene

ENSMUSG00000026867

Gene Name

GTPase activating protein and VPS9 domains 1

Synonyms

2010005B09Rik, 4432404J10Rik

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

IGL02636

Quality Score

Status

Chromosome

Chromosomal Location

34566190-34645297 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 34615416 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 409 (I409T)

Ref Sequence

ENSEMBL: ENSMUSP00000108723 (fasta)

Gene Model

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

AlphaFold

Q6PAR5

Predicted Effect

probably benign
Transcript: ENSMUST00000028224
AA Change: I409T

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000028224
Gene: ENSMUSG00000026867
AA Change: I409T

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: I409T

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000099864
Gene: ENSMUSG00000026867
AA Change: I409T

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: I409T

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000108723
Gene: ENSMUSG00000026867
AA Change: I409T

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

unknown
Transcript: ENSMUST00000113103
AA Change: I239T

SMART Domains

Protein: ENSMUSP00000108727
Gene: ENSMUSG00000026867
AA Change: I239T

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: ENSMUST00000137528
AA Change: I271T

SMART Domains

Protein: ENSMUSP00000120138
Gene: ENSMUSG00000026867
AA Change: I271T

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000169207

Coding Region Coverage

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 32 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Alms1	C	A	6: 85,605,636 (GRCm39)	Q1960K	probably benign	Het
Arhgef40	T	A	14: 52,234,865 (GRCm39)	V1056E	probably damaging	Het
Cdh26	T	A	2: 178,091,755 (GRCm39)	F105I	probably damaging	Het
Cep162	A	T	9: 87,130,432 (GRCm39)	D59E	possibly damaging	Het
Cngb3	A	T	4: 19,396,690 (GRCm39)	T348S	probably damaging	Het
Eci3	A	T	13: 35,130,963 (GRCm39)		probably null	Het
Golga2	T	C	2: 32,186,735 (GRCm39)		probably null	Het
Hoxd3	G	A	2: 74,577,298 (GRCm39)	A393T	probably benign	Het
Htr5a	T	C	5: 28,047,658 (GRCm39)	F71S	probably damaging	Het
Hyou1	T	C	9: 44,292,707 (GRCm39)		probably null	Het
Igsf6	C	A	7: 120,666,503 (GRCm39)		probably benign	Het
Klrb1c	C	A	6: 128,765,515 (GRCm39)	C25F	probably benign	Het
Lrguk	C	A	6: 34,067,123 (GRCm39)	T483K	probably damaging	Het
Lrpprc	A	T	17: 85,060,532 (GRCm39)		probably benign	Het
Lrrk1	A	T	7: 65,958,407 (GRCm39)		probably null	Het
Megf8	G	A	7: 25,057,857 (GRCm39)	G2098D	probably damaging	Het
Nfkbia	T	C	12: 55,537,958 (GRCm39)	Q165R	possibly damaging	Het
Nipsnap2	A	G	5: 129,822,354 (GRCm39)		probably benign	Het
Phykpl	C	T	11: 51,489,540 (GRCm39)	T382I	probably damaging	Het
Prdm10	A	G	9: 31,240,977 (GRCm39)	D206G	possibly damaging	Het
Rab26	T	C	17: 24,752,533 (GRCm39)	S9G	probably benign	Het
Sema3e	C	A	5: 14,275,670 (GRCm39)	N258K	probably benign	Het
Slfn10-ps	T	A	11: 82,920,971 (GRCm39)		noncoding transcript	Het
Tgm5	A	T	2: 120,907,277 (GRCm39)	C149S	probably damaging	Het
Timp4	C	T	6: 115,226,785 (GRCm39)		probably null	Het
Traf7	T	C	17: 24,731,964 (GRCm39)	K251E	probably benign	Het
Ugcg	G	T	4: 59,207,763 (GRCm39)	R34L	possibly damaging	Het
Unc13d	T	C	11: 115,964,444 (GRCm39)	H300R	probably damaging	Het
Vmn1r20	G	T	6: 57,408,746 (GRCm39)	C24F	probably benign	Het
Vmn2r13	T	C	5: 109,339,883 (GRCm39)	R31G	probably damaging	Het
Vsig10l	A	G	7: 43,113,002 (GRCm39)	T87A	possibly damaging	Het
Zfp353-ps	T	A	8: 42,535,477 (GRCm39)		noncoding transcript	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
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
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

Posted On

2015-04-16