Mutagenetix > Incidental Mutation

Incidental Mutation 'R5366:Vps9d1'

478138

Institutional Source

Beutler Lab

Gene Symbol

Vps9d1

Ensembl Gene

ENSMUSG00000001062

Gene Name

VPS9 domain containing 1

Synonyms

2410004N05Rik, 1300018I17Rik

MMRRC Submission

042944-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5366 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

123969095-123980961 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 123971853 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 584 (I584T)

Ref Sequence

ENSEMBL: ENSMUSP00000113575 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000117643] [ENSMUST00000118279] [ENSMUST00000122363] [ENSMUST00000127664] [ENSMUST00000155869]

AlphaFold

Q8C190

Predicted Effect

probably benign
Transcript: ENSMUST00000117643

SMART Domains

Protein: ENSMUSP00000113748
Gene: ENSMUSG00000001062

Domain	Start	End	E-Value	Type
low complexity region	96	108	N/A	INTRINSIC
coiled coil region	187	220	N/A	INTRINSIC
low complexity region	266	279	N/A	INTRINSIC
low complexity region	442	453	N/A	INTRINSIC
Pfam:VPS9	528	645	8.5e-27	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000118279
AA Change: I584T

PolyPhen 2 Score 0.119 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000113634
Gene: ENSMUSG00000001062
AA Change: I584T

Domain	Start	End	E-Value	Type
low complexity region	96	108	N/A	INTRINSIC
coiled coil region	187	220	N/A	INTRINSIC
low complexity region	266	279	N/A	INTRINSIC
low complexity region	442	453	N/A	INTRINSIC
Pfam:VPS9	528	645	1.2e-25	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000122363
AA Change: I584T

PolyPhen 2 Score 0.895 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000113575
Gene: ENSMUSG00000001062
AA Change: I584T

Domain	Start	End	E-Value	Type
low complexity region	96	108	N/A	INTRINSIC
coiled coil region	187	220	N/A	INTRINSIC
low complexity region	266	279	N/A	INTRINSIC
low complexity region	442	453	N/A	INTRINSIC
Pfam:VPS9	528	644	5.6e-27	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000124508

Predicted Effect

probably benign
Transcript: ENSMUST00000127664

SMART Domains

Protein: ENSMUSP00000118564
Gene: ENSMUSG00000092329

Domain	Start	End	E-Value	Type
Pfam:Glycos_transf_2	104	287	7.4e-31	PFAM
Pfam:Glyco_transf_7C	261	331	4.9e-8	PFAM
RICIN	406	531	9.28e-27	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127978

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000129591

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146136

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000149490

Predicted Effect

probably benign
Transcript: ENSMUST00000155869

SMART Domains

Protein: ENSMUSP00000122184
Gene: ENSMUSG00000001062

Domain	Start	End	E-Value	Type
low complexity region	96	108	N/A	INTRINSIC
coiled coil region	187	223	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155853

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137569

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000211876

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130965

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130275

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000181432

Meta Mutation Damage Score

0.1984

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 95.2%

Validation Efficiency

100% (77/77)

Allele List at MGI

Other mutations in this stock

Total: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb5	T	C	12: 118,831,665 (GRCm39)	N1229S	possibly damaging	Het
Adgre1	G	A	17: 57,709,817 (GRCm39)	C158Y	probably benign	Het
Ahnak	T	A	19: 8,994,099 (GRCm39)	S5128T	possibly damaging	Het
Ankrd36	T	A	11: 5,542,841 (GRCm39)	C322*	probably null	Het
Ano1	T	A	7: 144,207,946 (GRCm39)	T113S	possibly damaging	Het
Apeh	A	T	9: 107,969,005 (GRCm39)	S321T	probably benign	Het
Atg4d	T	A	9: 21,179,948 (GRCm39)	V273D	probably damaging	Het
Cacna2d4	A	G	6: 119,251,279 (GRCm39)	D489G	probably damaging	Het
Cd47	T	C	16: 49,716,736 (GRCm39)	F256L	probably damaging	Het
Cd84	A	T	1: 171,700,872 (GRCm39)	D211V	probably damaging	Het
Cfap46	A	G	7: 139,230,802 (GRCm39)	L942P	probably damaging	Het
Cfh	A	C	1: 140,063,973 (GRCm39)	C434W	probably damaging	Het
Chst2	T	C	9: 95,287,518 (GRCm39)	D276G	probably damaging	Het
Ctsq	T	C	13: 61,184,913 (GRCm39)	T258A	probably benign	Het
Degs1	C	A	1: 182,106,927 (GRCm39)	D111Y	probably benign	Het
Dhps	T	A	8: 85,801,413 (GRCm39)	D313E	probably damaging	Het
Dipk1c	T	A	18: 84,748,720 (GRCm39)	L106Q	probably damaging	Het
Dock9	A	G	14: 121,815,615 (GRCm39)	C1645R	probably damaging	Het
Efcab7	A	C	4: 99,761,931 (GRCm39)	D407A	possibly damaging	Het
Eif3a	G	T	19: 60,767,971 (GRCm39)	T189N	probably benign	Het
Ep300	T	A	15: 81,500,301 (GRCm39)	L57M	probably benign	Het
Exoc6b	T	A	6: 84,867,513 (GRCm39)	I300L	probably benign	Het
Fzd8	T	C	18: 9,213,880 (GRCm39)	S321P	probably damaging	Het
Garre1	A	T	7: 33,941,713 (GRCm39)	M657K	possibly damaging	Het
Gm9920	T	A	15: 54,975,705 (GRCm39)		probably benign	Het
Gucy2c	A	G	6: 136,697,739 (GRCm39)	I668T	probably damaging	Het
Irgc	C	T	7: 24,132,851 (GRCm39)		probably benign	Het
Jsrp1	G	T	10: 80,646,030 (GRCm39)	S143*	probably null	Het
Kctd4	T	C	14: 76,200,259 (GRCm39)	Y77H	probably damaging	Het
Klhdc1	T	A	12: 69,329,924 (GRCm39)	I351N	probably damaging	Het
Klra17	C	T	6: 129,851,858 (GRCm39)	E5K	possibly damaging	Het
Mapk8	A	T	14: 33,112,686 (GRCm39)	V211E	probably damaging	Het
Mdn1	C	T	4: 32,723,690 (GRCm39)	P2542L	probably damaging	Het
Mrc1	T	C	2: 14,326,725 (GRCm39)	Y1208H	probably benign	Het
Mrps16	A	T	14: 20,441,523 (GRCm39)	S94T	probably benign	Het
Muc5ac	A	G	7: 141,361,287 (GRCm39)	T1533A	probably benign	Het
Myh10	A	T	11: 68,651,518 (GRCm39)	D287V	probably damaging	Het
Obscn	T	C	11: 58,971,086 (GRCm39)	T2476A	probably damaging	Het
Olfm2	T	A	9: 20,579,708 (GRCm39)	T356S	probably benign	Het
Or4f60	T	C	2: 111,902,823 (GRCm39)	Y35C	possibly damaging	Het
P2rx2	T	A	5: 110,489,694 (GRCm39)	N108I	probably damaging	Het
Pbx4	A	T	8: 70,322,820 (GRCm39)	T309S	probably benign	Het
Phyhip	C	A	14: 70,704,295 (GRCm39)	H171Q	probably benign	Het
Pou4f3	A	G	18: 42,528,819 (GRCm39)	E254G	probably damaging	Het
Pxdn	C	A	12: 30,052,899 (GRCm39)	H845Q	probably damaging	Het
Rgcc	T	C	14: 79,529,123 (GRCm39)	T111A	probably benign	Het
Rptor	G	A	11: 119,734,539 (GRCm39)	G514D	probably damaging	Het
Scara5	CG	C	14: 65,997,111 (GRCm39)		probably null	Het
Sgsm1	C	A	5: 113,398,905 (GRCm39)	E722D	possibly damaging	Het
Soat1	A	T	1: 156,272,181 (GRCm39)	D101E	probably benign	Het
Spag5	T	A	11: 78,211,152 (GRCm39)		probably null	Het
Spata31	A	T	13: 65,068,273 (GRCm39)	E140D	probably damaging	Het
Srrm2	T	A	17: 24,037,678 (GRCm39)	S1537T	probably benign	Het
Stam2	G	A	2: 52,626,305 (GRCm39)		probably benign	Het
Tbc1d4	G	T	14: 101,845,412 (GRCm39)	T162K	possibly damaging	Het
Tmem163	A	C	1: 127,428,042 (GRCm39)		probably benign	Het
Tmem43	T	C	6: 91,455,240 (GRCm39)	V72A	probably benign	Het
Tmprss11c	G	A	5: 86,429,993 (GRCm39)	T24I	possibly damaging	Het
Trerf1	A	T	17: 47,626,116 (GRCm39)		noncoding transcript	Het
Trim44	A	G	2: 102,230,476 (GRCm39)	L185P	probably damaging	Het
Tspyl1	A	G	10: 34,158,341 (GRCm39)	D22G	possibly damaging	Het
Ttn	A	T	2: 76,641,587 (GRCm39)	L5176Q	possibly damaging	Het
Tyro3	G	A	2: 119,635,312 (GRCm39)	R201Q	probably damaging	Het
Ubxn2a	T	A	12: 4,930,741 (GRCm39)	K206N	probably benign	Het
Usp17lb	G	T	7: 104,489,615 (GRCm39)	H436Q	possibly damaging	Het
Vrk1	T	A	12: 106,022,078 (GRCm39)	M131K	possibly damaging	Het
Wdr87-ps	A	C	7: 29,232,964 (GRCm39)		noncoding transcript	Het
Zfp827	A	T	8: 79,912,333 (GRCm39)	K986N	possibly damaging	Het
Zswim4	A	G	8: 84,939,419 (GRCm39)	M821T	probably benign	Het

Other mutations in Vps9d1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00549:Vps9d1	APN	8	123,971,937 (GRCm39)	missense	probably damaging	1.00
IGL01112:Vps9d1	APN	8	123,972,769 (GRCm39)	missense	probably damaging	1.00
IGL01729:Vps9d1	APN	8	123,973,739 (GRCm39)	missense	probably damaging	1.00
R0568:Vps9d1	UTSW	8	123,973,487 (GRCm39)	missense	probably damaging	1.00
R1191:Vps9d1	UTSW	8	123,974,706 (GRCm39)	missense	possibly damaging	0.95
R1813:Vps9d1	UTSW	8	123,973,778 (GRCm39)	missense	probably damaging	0.99
R1896:Vps9d1	UTSW	8	123,973,778 (GRCm39)	missense	probably damaging	0.99
R2193:Vps9d1	UTSW	8	123,979,404 (GRCm39)	missense	probably damaging	1.00
R2256:Vps9d1	UTSW	8	123,971,860 (GRCm39)	missense	probably benign	0.18
R4305:Vps9d1	UTSW	8	123,974,976 (GRCm39)	intron	probably benign
R4458:Vps9d1	UTSW	8	123,974,487 (GRCm39)	missense	probably benign	0.30
R4707:Vps9d1	UTSW	8	123,975,351 (GRCm39)	critical splice donor site	probably benign
R5392:Vps9d1	UTSW	8	123,980,752 (GRCm39)	missense	probably damaging	0.99
R5423:Vps9d1	UTSW	8	123,974,704 (GRCm39)	critical splice donor site	probably null
R5645:Vps9d1	UTSW	8	123,974,487 (GRCm39)	missense	probably benign	0.30
R5647:Vps9d1	UTSW	8	123,975,598 (GRCm39)	missense	probably damaging	1.00
R5695:Vps9d1	UTSW	8	123,973,655 (GRCm39)	missense	probably benign
R5908:Vps9d1	UTSW	8	123,973,563 (GRCm39)	missense	probably benign	0.28
R6061:Vps9d1	UTSW	8	123,972,410 (GRCm39)	missense	probably damaging	0.99
R6250:Vps9d1	UTSW	8	123,974,947 (GRCm39)	critical splice acceptor site	probably null
R6416:Vps9d1	UTSW	8	123,975,378 (GRCm39)	missense	probably damaging	1.00
R6747:Vps9d1	UTSW	8	123,980,746 (GRCm39)	missense	probably damaging	1.00
R7049:Vps9d1	UTSW	8	123,973,882 (GRCm39)	nonsense	probably null
R7584:Vps9d1	UTSW	8	123,977,456 (GRCm39)	missense	probably damaging	1.00
R8321:Vps9d1	UTSW	8	123,975,544 (GRCm39)	missense	possibly damaging	0.47
R9178:Vps9d1	UTSW	8	123,975,574 (GRCm39)	missense	probably damaging	0.97
R9218:Vps9d1	UTSW	8	123,977,674 (GRCm39)	missense	probably benign	0.12
R9366:Vps9d1	UTSW	8	123,974,486 (GRCm39)	nonsense	probably null
R9542:Vps9d1	UTSW	8	123,970,522 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GCCAGAGGACACTGCTATAG -3'
(R):5'- CACACCGGGTCCTTTAAGTC -3'

Sequencing Primer
(F):5'- CTTGTTCAGATGGACTGGAACACAC -3'
(R):5'- AAGTCTTCCTGCCCTTGTCAGATAC -3'

Posted On

2017-05-26