Mutagenetix > Incidental Mutation

Incidental Mutation 'R6747:Vps9d1'

530593

Institutional Source

Beutler Lab

Gene Symbol

Vps9d1

Ensembl Gene

ENSMUSG00000001062

Gene Name

VPS9 domain containing 1

Synonyms

2410004N05Rik, 1300018I17Rik

MMRRC Submission

044864-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6747 (G1)

Quality Score

184.009

Status

Validated

Chromosome

Chromosomal Location

123969095-123980961 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 123980746 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 27 (D27G)

Ref Sequence

ENSEMBL: ENSMUSP00000113575 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000001092] [ENSMUST00000117643] [ENSMUST00000118279] [ENSMUST00000122363] [ENSMUST00000127664] [ENSMUST00000155869] [ENSMUST00000154450]

AlphaFold

Q8C190

Predicted Effect

probably benign
Transcript: ENSMUST00000001092

SMART Domains

Protein: ENSMUSP00000001092
Gene: ENSMUSG00000001065

Domain	Start	End	E-Value	Type
low complexity region	18	41	N/A	INTRINSIC
low complexity region	59	72	N/A	INTRINSIC
Pfam:zf-AD	79	159	1.2e-13	PFAM
low complexity region	402	422	N/A	INTRINSIC
ZnF_C2H2	434	458	2.24e-3	SMART
ZnF_C2H2	465	490	6.67e-2	SMART
ZnF_C2H2	496	518	1.38e-3	SMART
ZnF_C2H2	524	546	1.82e-3	SMART
ZnF_C2H2	554	577	4.79e-3	SMART
low complexity region	586	602	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000117643
AA Change: D27G

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

SMART Domains

Protein: ENSMUSP00000113748
Gene: ENSMUSG00000001062
AA Change: D27G

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: D27G

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

SMART Domains

Protein: ENSMUSP00000113634
Gene: ENSMUSG00000001062
AA Change: D27G

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: D27G

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

SMART Domains

Protein: ENSMUSP00000113575
Gene: ENSMUSG00000001062
AA Change: D27G

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

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: ENSMUST00000129591

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130275

Predicted Effect

possibly damaging
Transcript: ENSMUST00000155869
AA Change: D27G

PolyPhen 2 Score 0.890 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000122184
Gene: ENSMUSG00000001062
AA Change: D27G

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: ENSMUST00000149490

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150356

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146136

Predicted Effect

probably benign
Transcript: ENSMUST00000154450

SMART Domains

Protein: ENSMUSP00000119771
Gene: ENSMUSG00000001065

Domain	Start	End	E-Value	Type
low complexity region	18	41	N/A	INTRINSIC
low complexity region	59	72	N/A	INTRINSIC
Pfam:zf-AD	79	159	1.9e-14	PFAM
low complexity region	183	203	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156896

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000211828

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146158

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137569

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.5%
20x: 96.0%

Validation Efficiency

97% (68/70)

Allele List at MGI

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca4	C	T	3: 121,919,962 (GRCm39)		probably null	Het
Acyp1	C	T	12: 85,325,679 (GRCm39)	V107I	probably null	Het
Aftph	T	C	11: 20,676,144 (GRCm39)		probably null	Het
Agtpbp1	A	T	13: 59,692,167 (GRCm39)		probably null	Het
Arhgap15	C	A	2: 44,006,689 (GRCm39)	P269T	probably damaging	Het
Arhgap30	T	C	1: 171,235,297 (GRCm39)	V557A	probably damaging	Het
Asb3	T	A	11: 31,031,493 (GRCm39)	M410K	probably benign	Het
B4galnt2	T	C	11: 95,759,460 (GRCm39)		probably null	Het
Birc2	A	G	9: 7,860,262 (GRCm39)		probably null	Het
Cav2	A	T	6: 17,286,950 (GRCm39)	N69Y	probably damaging	Het
Cc2d2b	G	A	19: 40,784,111 (GRCm39)	C826Y	probably benign	Het
Cenpf	T	A	1: 189,385,051 (GRCm39)	T2410S	probably benign	Het
Chchd1	A	G	14: 20,753,448 (GRCm39)	D24G	probably benign	Het
Cmip	G	A	8: 118,163,618 (GRCm39)	G450S	probably benign	Het
Col11a1	C	T	3: 114,006,099 (GRCm39)	Q534*	probably null	Het
Col3a1	G	T	1: 45,377,782 (GRCm39)		probably benign	Het
Cox4i1	T	C	8: 121,399,969 (GRCm39)	I31T	possibly damaging	Het
Cstf3	G	T	2: 104,477,112 (GRCm39)	V168F	probably damaging	Het
Dapk1	T	C	13: 60,873,154 (GRCm39)	I352T	probably benign	Het
Ddx52	T	C	11: 83,846,128 (GRCm39)	V456A	probably damaging	Het
Dmxl2	A	T	9: 54,323,372 (GRCm39)	H1337Q	probably damaging	Het
Dnah7a	T	C	1: 53,675,221 (GRCm39)	T369A	probably benign	Het
Dppa1	T	A	11: 46,516,422 (GRCm39)	I8F	unknown	Het
Ebf1	G	T	11: 44,774,641 (GRCm39)	V213F	probably damaging	Het
Foxb2	C	A	19: 16,850,197 (GRCm39)	E270*	probably null	Het
Gclc	A	T	9: 77,695,527 (GRCm39)	R450W	probably damaging	Het
Grin2d	T	C	7: 45,511,692 (GRCm39)	E251G	probably damaging	Het
Hal	A	T	10: 93,336,539 (GRCm39)	N423Y	probably damaging	Het
Krtap4-8	T	A	11: 99,670,917 (GRCm39)	I185F	unknown	Het
Lrp3	T	A	7: 34,910,862 (GRCm39)	Q61L	probably benign	Het
Met	A	C	6: 17,571,466 (GRCm39)	Q1296H	probably damaging	Het
Mphosph9	T	A	5: 124,435,762 (GRCm39)	N557I	possibly damaging	Het
Mrpl46	C	A	7: 78,432,729 (GRCm39)	W16C	probably benign	Het
Myh13	G	A	11: 67,241,245 (GRCm39)	R874Q	probably damaging	Het
Nelfb	G	A	2: 25,093,393 (GRCm39)	T453I	probably benign	Het
Nos2	A	G	11: 78,843,780 (GRCm39)	D909G	probably damaging	Het
Nr5a2	T	C	1: 136,810,082 (GRCm39)	E431G	possibly damaging	Het
Nsmce2	A	G	15: 59,463,573 (GRCm39)	D149G	probably benign	Het
Or52b1	C	T	7: 104,979,234 (GRCm39)	R55H	probably benign	Het
Or5ac21	T	C	16: 59,124,004 (GRCm39)	F164L	probably benign	Het
Pcbp4	C	A	9: 106,337,847 (GRCm39)		probably null	Het
Peg10	A	G	6: 4,757,137 (GRCm39)		probably benign	Het
Pms2	C	T	5: 143,862,237 (GRCm39)	P154L	probably benign	Het
Pou6f2	A	C	13: 18,303,772 (GRCm39)	L112R	probably benign	Het
Pramel30	T	C	4: 144,059,548 (GRCm39)	W420R	probably benign	Het
Prdm6	A	T	18: 53,598,118 (GRCm39)		probably benign	Het
Prob1	G	A	18: 35,788,207 (GRCm39)	R12W	probably damaging	Het
Rif1	T	A	2: 51,968,275 (GRCm39)		probably null	Het
Rpl9-ps6	A	G	19: 32,443,543 (GRCm39)	S137P	probably benign	Het
Rsf1	GGCG	GGCGACGGCAGCG	7: 97,229,113 (GRCm39)		probably benign	Homo
Sec23ip	A	G	7: 128,354,573 (GRCm39)		silent	Het
Slc38a9	T	C	13: 112,826,714 (GRCm39)	C151R	probably benign	Het
Slc39a8	T	C	3: 135,554,941 (GRCm39)		probably null	Het
Slc6a18	C	A	13: 73,826,110 (GRCm39)		probably benign	Het
Snw1	T	C	12: 87,511,480 (GRCm39)	D57G	probably damaging	Het
Sox6	C	G	7: 115,140,966 (GRCm39)	R505P	probably damaging	Het
Speg	T	C	1: 75,387,039 (GRCm39)		probably null	Het
Spire2	C	T	8: 124,083,585 (GRCm39)	R190C	probably damaging	Het
Stard9	A	C	2: 120,528,864 (GRCm39)	H1707P	possibly damaging	Het
Tenm3	G	T	8: 48,796,278 (GRCm39)	T237K	probably damaging	Het
Themis2	T	A	4: 132,523,573 (GRCm39)	E31V	possibly damaging	Het
Trim56	T	G	5: 137,143,375 (GRCm39)	Q47P	probably damaging	Het
Trim58	T	C	11: 58,542,090 (GRCm39)	I350T	probably benign	Het
Ttll7	C	T	3: 146,649,811 (GRCm39)	P639S	probably benign	Het
Ubxn6	A	G	17: 56,377,650 (GRCm39)		probably null	Het
Vmn2r114	A	T	17: 23,528,850 (GRCm39)	F417L	probably benign	Het
Vmn2r29	T	A	7: 7,234,421 (GRCm39)	M822L	probably benign	Het
Wdr3	C	T	3: 100,046,040 (GRCm39)	R931Q	probably damaging	Het
Whamm	G	A	7: 81,228,050 (GRCm39)		probably null	Het
Zcchc24	T	C	14: 25,757,457 (GRCm39)	H142R	probably damaging	Het
Zfp292	T	C	4: 34,806,894 (GRCm39)	K2050R	probably damaging	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
R5366:Vps9d1	UTSW	8	123,971,853 (GRCm39)	missense	possibly damaging	0.89
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
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'- CAGGTAAATCTAGGCCCAGTG -3'
(R):5'- AGGTGACAAGAGCCACTGAC -3'

Sequencing Primer
(F):5'- TAAATCTAGGCCCAGTGCGAGC -3'
(R):5'- TAAACCCAAGTCTGCGCGG -3'

Posted On

2018-08-01