Mutagenetix > Incidental Mutation

Incidental Mutation 'R5645:Vps9d1'

441066

Institutional Source

Beutler Lab

Gene Symbol

Vps9d1

Ensembl Gene

ENSMUSG00000001062

Gene Name

VPS9 domain containing 1

Synonyms

MMRRC Submission

043293-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5645 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

123242356-123254348 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 123247748 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 267 (S267P)

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
AA Change: S267P

PolyPhen 2 Score 0.304 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000113748
Gene: ENSMUSG00000001062
AA Change: S267P

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: S267P

PolyPhen 2 Score 0.036 (Sensitivity: 0.94; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000113634
Gene: ENSMUSG00000001062
AA Change: S267P

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 benign
Transcript: ENSMUST00000122363
AA Change: S267P

PolyPhen 2 Score 0.304 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000113575
Gene: ENSMUSG00000001062
AA Change: S267P

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

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.5%
20x: 95.9%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700102P08Rik	A	G	9: 108,397,204	I169V	probably damaging	Het
2310007B03Rik	T	C	1: 93,152,946	T413A	probably damaging	Het
4930503B20Rik	C	T	3: 146,650,509	E215K	probably damaging	Het
5830411N06Rik	G	A	7: 140,248,940	V171I	possibly damaging	Het
Abca6	T	C	11: 110,250,408	E29G	probably damaging	Het
Acsm1	A	G	7: 119,640,697	H288R	probably damaging	Het
Adamts12	A	G	15: 11,277,420	T707A	possibly damaging	Het
Adcy2	C	A	13: 68,729,202		probably null	Het
Agbl4	A	T	4: 111,657,330	I513F	possibly damaging	Het
Ak5	A	T	3: 152,656,033	M84K	possibly damaging	Het
Akap1	T	C	11: 88,845,627	T103A	probably benign	Het
Akap9	A	G	5: 4,050,590	T2751A	probably benign	Het
Amer3	A	T	1: 34,588,381	H567L	possibly damaging	Het
Ano6	A	G	15: 95,920,351	Y325C	probably benign	Het
Apba2	A	G	7: 64,695,806	E248G	possibly damaging	Het
Asap2	T	A	12: 21,265,982	V967E	probably damaging	Het
Boc	A	G	16: 44,499,661	V320A	probably damaging	Het
Car13	T	A	3: 14,645,120	Y41N	possibly damaging	Het
Ccdc162	T	C	10: 41,552,356	T1976A	probably benign	Het
Cep295	A	T	9: 15,332,794	H1455Q	probably damaging	Het
Cep295	C	A	9: 15,335,108	S684I	possibly damaging	Het
Cr2	G	T	1: 195,154,273	H861N	probably damaging	Het
Cul5	T	C	9: 53,622,943	I630V	probably benign	Het
Cyp2c37	G	A	19: 39,994,152	V145I	probably benign	Het
Dnmt1	G	A	9: 20,922,147	T500M	probably damaging	Het
Fam161a	T	A	11: 23,015,725	I6N	probably damaging	Het
Fam214a	T	A	9: 75,025,679	V976E	probably damaging	Het
Fry	T	C	5: 150,380,867	V574A	probably damaging	Het
Glb1l3	G	T	9: 26,824,826	L553I	probably benign	Het
Gm1123	T	C	9: 99,014,191	D212G	probably benign	Het
Grin2a	T	A	16: 9,992,226	D103V	probably damaging	Het
Heg1	A	G	16: 33,706,963	I98V	probably benign	Het
Hmcn2	C	A	2: 31,420,812	T3356N	possibly damaging	Het
Hpf1	T	G	8: 60,896,800	I154S	possibly damaging	Het
Ifnar2	A	G	16: 91,404,227	D452G	possibly damaging	Het
Ikbkap	T	C	4: 56,776,920	T626A	possibly damaging	Het
Iqcc	A	T	4: 129,616,527	H398Q	possibly damaging	Het
Iqgap3	T	C	3: 88,117,699	I669T	probably damaging	Het
Itgae	A	G	11: 73,129,248	T859A	probably damaging	Het
Kansl1l	T	C	1: 66,801,344	M266V	probably benign	Het
Kbtbd3	A	G	9: 4,331,426	D600G	possibly damaging	Het
Klf13	G	A	7: 63,891,600		probably benign	Het
Kmt2d	A	G	15: 98,844,397		probably benign	Het
Lama1	A	G	17: 67,802,948	D2188G	probably damaging	Het
Leng8	A	G	7: 4,145,274	T682A	probably damaging	Het
Mslnl	G	T	17: 25,737,842	G34V	possibly damaging	Het
Mycbp2	A	T	14: 103,188,608	S2360R	probably damaging	Het
Mycbp2	C	A	14: 103,188,615		probably null	Het
Nkx2-2	T	C	2: 147,184,399	T140A	probably damaging	Het
Olfr1233	A	T	2: 89,339,705	V199E	possibly damaging	Het
Olfr745	T	C	14: 50,643,067	V262A	probably benign	Het
Oser1	C	T	2: 163,407,045	R79H	probably damaging	Het
Pfas	A	G	11: 68,991,132	V909A	probably damaging	Het
Pkhd1l1	A	G	15: 44,532,992	E1970G	probably benign	Het
Prph2	G	T	17: 46,910,667		probably benign	Het
Rusc2	G	T	4: 43,425,758	A1288S	probably benign	Het
Sdha	A	G	13: 74,323,839		probably null	Het
Sec16a	T	G	2: 26,439,895	T703P	probably benign	Het
Senp7	T	A	16: 56,173,208	N724K	possibly damaging	Het
Skint1	A	G	4: 112,025,502	I248V	probably benign	Het
Slc9a5	T	C	8: 105,357,013	V395A	probably benign	Het
Slco1a4	T	C	6: 141,834,659	N135S	possibly damaging	Het
Sncaip	A	G	18: 52,894,956	I412M	probably damaging	Het
Tacc2	A	T	7: 130,624,051	D841V	possibly damaging	Het
Tekt1	A	T	11: 72,351,837	H281Q	probably benign	Het
Tex46	G	T	4: 136,612,917	M104I	probably benign	Het
Tjp3	T	C	10: 81,278,620		probably null	Het
Treh	A	G	9: 44,682,678	Y154C	probably damaging	Het
Trim80	T	A	11: 115,446,785	L428Q	probably damaging	Het
Trpm6	A	G	19: 18,853,604	K1278E	probably damaging	Het
Usp34	T	C	11: 23,375,024	M990T	possibly damaging	Het
Ywhae	T	C	11: 75,756,924	M160T	probably benign	Het
Zcchc11	G	A	4: 108,557,373	R49H	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
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
R6061:Vps9d1	UTSW	8	123245671	missense	probably damaging	0.99
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'- TAGTGTGACCCATGCAATCTGG -3'
(R):5'- TCACATGGGCCTATAGGACTC -3'

Sequencing Primer
(F):5'- CCATGCAATCTGGGGAAGC -3'
(R):5'- ACATGGGCCTATAGGACTCAGTTC -3'

Posted On

2016-11-08