Mutagenetix > Incidental Mutation

Incidental Mutation 'R7584:Vps9d1'

586971

Institutional Source

Beutler Lab

Gene Symbol

Vps9d1

Ensembl Gene

ENSMUSG00000001062

Gene Name

VPS9 domain containing 1

Synonyms

2410004N05Rik, 1300018I17Rik

MMRRC Submission

045667-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7584 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

123969095-123980961 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 123977456 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Serine at position 131 (F131S)

Ref Sequence

ENSEMBL: ENSMUSP00000113634 (fasta)

Gene Model

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

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: F131S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000113748
Gene: ENSMUSG00000001062
AA Change: F131S

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: F131S

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000113634
Gene: ENSMUSG00000001062
AA Change: F131S

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: F131S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000113575
Gene: ENSMUSG00000001062
AA Change: F131S

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

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

probably damaging
Transcript: ENSMUST00000155869
AA Change: F131S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000122184
Gene: ENSMUSG00000001062
AA Change: F131S

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

99% (74/75)

Allele List at MGI

Other mutations in this stock

Total: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc10	A	G	17: 46,626,304 (GRCm39)		probably null	Het
Actrt3	T	C	3: 30,652,356 (GRCm39)	K246R	probably benign	Het
Adam23	T	A	1: 63,584,621 (GRCm39)	V343D	probably damaging	Het
Ak2	T	C	4: 128,893,005 (GRCm39)	S55P	probably damaging	Het
Ank2	G	A	3: 126,739,777 (GRCm39)	Q2036*	probably null	Het
Ano10	A	G	9: 122,104,597 (GRCm39)	I40T	probably benign	Het
Aoc2	T	A	11: 101,217,005 (GRCm39)	C363S	possibly damaging	Het
Aplp2	A	T	9: 31,069,077 (GRCm39)	V584E	possibly damaging	Het
Arhgap32	A	T	9: 32,168,263 (GRCm39)	T749S	probably benign	Het
Atm	A	T	9: 53,424,427 (GRCm39)	F625I	probably damaging	Het
Atr	T	C	9: 95,824,766 (GRCm39)	L2387P	probably damaging	Het
Barhl1	C	T	2: 28,799,803 (GRCm39)	G274D	probably damaging	Het
Bcl2a1a	A	T	9: 88,839,345 (GRCm39)	D81V	probably damaging	Het
Ccdc63	T	G	5: 122,251,267 (GRCm39)	D381A	possibly damaging	Het
Col12a1	A	G	9: 79,610,578 (GRCm39)		probably null	Het
Crat	C	T	2: 30,294,577 (GRCm39)	R497Q	probably benign	Het
Cyp4b1	T	A	4: 115,485,884 (GRCm39)	D351V	probably damaging	Het
D130043K22Rik	A	G	13: 25,056,353 (GRCm39)	S562G	probably damaging	Het
Dgkb	T	A	12: 38,189,391 (GRCm39)		probably null	Het
Dmbt1	C	T	7: 130,690,481 (GRCm39)	Q905*	probably null	Het
Dnajc21	A	C	15: 10,462,381 (GRCm39)	Y81*	probably null	Het
Dnali1	T	C	4: 124,959,331 (GRCm39)	T21A	probably benign	Het
Dpp8	A	T	9: 64,986,064 (GRCm39)	L851F	probably damaging	Het
Dpt	T	C	1: 164,646,477 (GRCm39)	Y149H	probably benign	Het
Ep300	T	C	15: 81,512,627 (GRCm39)	V983A	unknown	Het
Faf1	C	T	4: 109,783,154 (GRCm39)	R549C	probably damaging	Het
Gcm1	A	G	9: 77,971,749 (GRCm39)	N230S	possibly damaging	Het
Gm10803	T	A	2: 93,394,513 (GRCm39)	I95N	probably damaging	Het
Hectd4	T	A	5: 121,456,798 (GRCm39)	I721N	possibly damaging	Het
Hsp90ab1	T	C	17: 45,881,197 (GRCm39)	H315R	probably damaging	Het
Igkv10-95	T	A	6: 68,657,740 (GRCm39)	S85R	possibly damaging	Het
Katnip	G	T	7: 125,469,838 (GRCm39)	V1436L	probably damaging	Het
Kcnq5	T	C	1: 21,472,545 (GRCm39)	T901A	probably benign	Het
Kremen1	C	T	11: 5,144,964 (GRCm39)	V471M	possibly damaging	Het
Lama2	C	A	10: 26,980,257 (GRCm39)	D1853Y	possibly damaging	Het
Lrif1	A	G	3: 106,639,217 (GRCm39)	T76A	probably benign	Het
Lrrtm2	T	A	18: 35,345,818 (GRCm39)	I495F	possibly damaging	Het
Ltbr	G	T	6: 125,284,204 (GRCm39)	Q413K	probably benign	Het
Ms4a20	A	G	19: 11,087,725 (GRCm39)	F69L	possibly damaging	Het
Myrfl	T	A	10: 116,664,902 (GRCm39)	Y376F	probably damaging	Het
Nup50l	A	C	6: 96,142,373 (GRCm39)	L224V	probably benign	Het
Nup98	G	T	7: 101,825,596 (GRCm39)	N414K	probably benign	Het
Nynrin	A	G	14: 56,109,041 (GRCm39)	T1383A	probably damaging	Het
Or4c15	G	A	2: 88,760,149 (GRCm39)	P170L	probably damaging	Het
Or5j1	A	T	2: 86,879,478 (GRCm39)	I34N	probably benign	Het
Or6c208	T	A	10: 129,223,901 (GRCm39)	I133N	probably damaging	Het
Or7g27	C	A	9: 19,250,569 (GRCm39)	T271K	possibly damaging	Het
Or8b1d	G	T	9: 38,558,191 (GRCm39)	P210T	possibly damaging	Het
Pcdhb5	T	A	18: 37,455,425 (GRCm39)	S602T	possibly damaging	Het
Sall3	A	G	18: 81,017,745 (GRCm39)	F61S	probably benign	Het
Scube1	G	T	15: 83,606,088 (GRCm39)	C61*	probably null	Het
Sec31b	T	C	19: 44,519,995 (GRCm39)		probably null	Het
Sec31b	T	C	19: 44,531,762 (GRCm39)	D49G	probably damaging	Het
Skic2	A	G	17: 35,060,651 (GRCm39)	I822T	possibly damaging	Het
Slc19a3	C	T	1: 83,000,469 (GRCm39)	V183M	possibly damaging	Het
Slc41a2	T	C	10: 83,152,653 (GRCm39)		probably benign	Het
Sphk2	C	A	7: 45,361,931 (GRCm39)	V169L	probably damaging	Het
Synpo	C	A	18: 60,729,349 (GRCm39)	R951L	probably damaging	Het
Tbc1d9b	G	A	11: 50,061,543 (GRCm39)	C1017Y	probably damaging	Het
Tmtc4	C	A	14: 123,215,563 (GRCm39)	V28F	probably benign	Het
Tprkb	A	G	6: 85,905,809 (GRCm39)	I165V	probably benign	Het
Ttc23l	T	A	15: 10,533,794 (GRCm39)	I250F	probably damaging	Het
Tut4	T	C	4: 108,336,543 (GRCm39)	V89A	probably benign	Het
Ubr3	G	A	2: 69,821,847 (GRCm39)	V1370I	probably damaging	Het
Ush2a	A	G	1: 188,460,306 (GRCm39)		probably null	Het
Usp9y	T	C	Y: 1,384,451 (GRCm39)	Y689C	probably damaging	Het
Vmn1r56	A	T	7: 5,198,895 (GRCm39)	Y241N	probably damaging	Het
Vmn2r6	T	C	3: 64,472,683 (GRCm39)	T13A	probably benign	Het
Vmn2r92	T	A	17: 18,387,028 (GRCm39)	N122K	probably benign	Het
Vwa8	A	C	14: 79,219,674 (GRCm39)		probably null	Het
Wfdc16	A	T	2: 164,480,547 (GRCm39)		probably null	Het
Zbtb41	T	A	1: 139,351,795 (GRCm39)	Y303N	probably benign	Het
Zbtb5	T	C	4: 44,993,678 (GRCm39)	T569A	probably benign	Het
Zfp111	A	G	7: 23,898,025 (GRCm39)	S530P	possibly 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
R6747:Vps9d1	UTSW	8	123,980,746 (GRCm39)	missense	probably damaging	1.00
R7049:Vps9d1	UTSW	8	123,973,882 (GRCm39)	nonsense	probably null
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'- TGCACTTGCTTCTGTCAGG -3'
(R):5'- AGCTGGCTGAACAGTGTCTG -3'

Sequencing Primer
(F):5'- ACTTGCTTCTGTCAGGCCAGG -3'
(R):5'- CCAAGCTTGGTGGGTACAC -3'

Posted On

2019-10-24