Mutagenetix > Incidental Mutation

Incidental Mutation 'R6061:Vps9d1'

483238

Institutional Source

Beutler Lab

Gene Symbol

Vps9d1

Ensembl Gene

ENSMUSG00000001062

Gene Name

VPS9 domain containing 1

Synonyms

MMRRC Submission

044226-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6061 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

123242356-123254348 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 123245671 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 497 (M497K)

Ref Sequence

ENSEMBL: ENSMUSP00000113634 (fasta)

Gene Model

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

AlphaFold

Q8C190

Predicted Effect

probably damaging
Transcript: ENSMUST00000117643
AA Change: M497K

PolyPhen 2 Score 0.961 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000113748
Gene: ENSMUSG00000001062
AA Change: M497K

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 damaging
Transcript: ENSMUST00000118279
AA Change: M497K

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000113634
Gene: ENSMUSG00000001062
AA Change: M497K

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

probably damaging
Transcript: ENSMUST00000122363
AA Change: M497K

PolyPhen 2 Score 0.961 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000113575
Gene: ENSMUSG00000001062
AA Change: M497K

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: ENSMUST00000130275

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130965

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137569

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146136

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000149490

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155853

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: ENSMUST00000181432

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000211876

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.7%
20x: 92.9%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 42 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A2ml1	A	C	6: 128,568,712	F484C	probably damaging	Het
Cdsn	A	G	17: 35,554,906	S111G	unknown	Het
Ctnnal1	T	C	4: 56,812,349	T726A	probably benign	Het
Cyp2j11	T	A	4: 96,348,616		probably benign	Het
Ddx60	T	A	8: 62,023,241	M1541K	probably null	Het
Dnah14	C	T	1: 181,709,051	P2420S	probably damaging	Het
Doxl2	A	C	6: 48,976,601	I487L	probably benign	Het
Fhit	T	C	14: 9,573,435	E205G	probably benign	Het
Glipr1l1	C	T	10: 112,076,170	T203M	probably benign	Het
Gm4353	T	A	7: 116,084,269	D97V	probably benign	Het
Gprc6a	A	T	10: 51,615,811	I543K	probably damaging	Het
Ifi205	T	C	1: 174,027,264	T110A	possibly damaging	Het
Med27	T	A	2: 29,509,441	S95T	probably damaging	Het
Mocs1	T	C	17: 49,450,313	S308P	probably damaging	Het
Mrpl11	C	T	19: 4,963,369	S88F	possibly damaging	Het
Nav3	A	T	10: 109,866,984	Y229*	probably null	Het
Olfr138	A	G	17: 38,274,881	M37V	probably benign	Het
Olfr38	A	T	6: 42,762,965	L304F	probably damaging	Het
Olfr569	C	A	7: 102,887,951	L67F	probably benign	Het
Olfr668	C	T	7: 104,925,392	R124H	probably benign	Het
Olfr996	T	A	2: 85,579,542	M101K	possibly damaging	Het
Pear1	A	G	3: 87,755,931	I460T	probably benign	Het
Phc3	T	A	3: 30,914,529	K816N	probably damaging	Het
Phf19	T	A	2: 34,897,117	D445V	probably damaging	Het
Pkd2l2	T	C	18: 34,430,689	F486L	probably damaging	Het
Plagl1	G	T	10: 13,127,895		probably benign	Het
Prkca	A	G	11: 108,057,845	I106T	probably benign	Het
Ptpn3	C	T	4: 57,248,681	G218R	probably damaging	Het
Ptx3	A	G	3: 66,224,709	D217G	possibly damaging	Het
Rab3d	T	C	9: 21,910,519	T209A	probably benign	Het
Rfx2	A	G	17: 56,777,473	F642S	possibly damaging	Het
Rhpn2	T	A	7: 35,376,211	M271K	possibly damaging	Het
Serpinb6b	A	G	13: 32,977,994	T259A	probably damaging	Het
Speer3	G	A	5: 13,794,691	V123M	possibly damaging	Het
Svil	T	G	18: 5,106,724	V1855G	probably damaging	Het
Thbs4	A	G	13: 92,751,795	F950L	probably benign	Het
Tiparp	T	C	3: 65,553,243	V551A	probably damaging	Het
Vmn2r71	T	A	7: 85,619,274	D228E	probably benign	Het
Vmn2r85	T	C	10: 130,425,662	I269V	probably benign	Het
Wnt5b	A	G	6: 119,433,642	V241A	probably damaging	Het
Xdh	T	C	17: 73,921,347	N353S	probably damaging	Het
Zfp526	C	T	7: 25,226,332	T672M	probably damaging	Het

Other mutations in Vps9d1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00549:Vps9d1	APN	8	123245198	missense	probably damaging	1.00
IGL01112:Vps9d1	APN	8	123246030	missense	probably damaging	1.00
IGL01729:Vps9d1	APN	8	123247000	missense	probably damaging	1.00
R0568:Vps9d1	UTSW	8	123246748	missense	probably damaging	1.00
R1191:Vps9d1	UTSW	8	123247967	missense	possibly damaging	0.95
R1813:Vps9d1	UTSW	8	123247039	missense	probably damaging	0.99
R1896:Vps9d1	UTSW	8	123247039	missense	probably damaging	0.99
R2193:Vps9d1	UTSW	8	123252665	missense	probably damaging	1.00
R2256:Vps9d1	UTSW	8	123245121	missense	probably benign	0.18
R4305:Vps9d1	UTSW	8	123248237	intron	probably benign
R4458:Vps9d1	UTSW	8	123247748	missense	probably benign	0.30
R4707:Vps9d1	UTSW	8	123248612	critical splice donor site	probably benign
R5366:Vps9d1	UTSW	8	123245114	missense	possibly damaging	0.89
R5392:Vps9d1	UTSW	8	123254013	missense	probably damaging	0.99
R5423:Vps9d1	UTSW	8	123247965	critical splice donor site	probably null
R5645:Vps9d1	UTSW	8	123247748	missense	probably benign	0.30
R5647:Vps9d1	UTSW	8	123248859	missense	probably damaging	1.00
R5695:Vps9d1	UTSW	8	123246916	missense	probably benign
R5908:Vps9d1	UTSW	8	123246824	missense	probably benign	0.28
R6250:Vps9d1	UTSW	8	123248208	critical splice acceptor site	probably null
R6416:Vps9d1	UTSW	8	123248639	missense	probably damaging	1.00
R6747:Vps9d1	UTSW	8	123254007	missense	probably damaging	1.00
R7049:Vps9d1	UTSW	8	123247143	nonsense	probably null
R7584:Vps9d1	UTSW	8	123250717	missense	probably damaging	1.00
R8321:Vps9d1	UTSW	8	123248805	missense	possibly damaging	0.47
R9178:Vps9d1	UTSW	8	123248835	missense	probably damaging	0.97
R9218:Vps9d1	UTSW	8	123250935	missense	probably benign	0.12
R9366:Vps9d1	UTSW	8	123247747	nonsense	probably null
R9542:Vps9d1	UTSW	8	123243783	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TTGCTTAGTGAGGGACCTGC -3'
(R):5'- CAAGTGTGCAGGTGGCTAAG -3'

Sequencing Primer
(F):5'- ACCTGCAGGCTAGCACAG -3'
(R):5'- GCTAAGCCACTTATCTGTCTAGAGAC -3'

Posted On

2017-07-14