Mutagenetix > Incidental Mutations

Incidental Mutation 'R6416:Vps9d1'

517936

Institutional Source

Beutler Lab

Gene Symbol

Vps9d1

Ensembl Gene

ENSMUSG00000001062

Gene Name

VPS9 domain containing 1

Synonyms

MMRRC Submission

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6416 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

123242356-123254348 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 123248639 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Glycine at position 194 (V194G)

Ref Sequence

ENSEMBL: ENSMUSP00000122184 (fasta)

Gene Model

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

AlphaFold

Q8C190

Predicted Effect

possibly damaging
Transcript: ENSMUST00000117643
AA Change: V194G

PolyPhen 2 Score 0.925 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000113748
Gene: ENSMUSG00000001062
AA Change: V194G

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

possibly damaging
Transcript: ENSMUST00000118279
AA Change: V194G

PolyPhen 2 Score 0.848 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000113634
Gene: ENSMUSG00000001062
AA Change: V194G

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: V194G

PolyPhen 2 Score 0.925 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000113575
Gene: ENSMUSG00000001062
AA Change: V194G

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

probably damaging
Transcript: ENSMUST00000155869
AA Change: V194G

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

SMART Domains

Protein: ENSMUSP00000122184
Gene: ENSMUSG00000001062
AA Change: V194G

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

Meta Mutation Damage Score

0.1055

Coding Region Coverage

1x: 100.0%
3x: 99.8%
10x: 98.4%
20x: 94.6%

Validation Efficiency

99% (67/68)

Allele List at MGI

Other mutations in this stock

Total: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310061N02Rik	C	A	16: 88,707,891	R6L	unknown	Het
Anxa11	A	G	14: 25,874,270	Q235R	possibly damaging	Het
Ap2b1	T	A	11: 83,308,239	M1K	probably null	Het
Atl2	G	A	17: 79,850,223	T563I	probably benign	Het
Azin1	A	T	15: 38,492,343	S307R	possibly damaging	Het
Ccdc153	A	G	9: 44,245,780	T118A	probably benign	Het
Chac1	G	A	2: 119,353,534	V206I	probably damaging	Het
Chrm3	A	G	13: 9,877,662	V446A	probably benign	Het
Cped1	T	C	6: 22,123,649	F467S	probably damaging	Het
Csmd3	G	A	15: 48,673,560	P82L	probably damaging	Het
Ddx60	T	A	8: 61,977,950	S840T	probably benign	Het
Ddx60	C	T	8: 61,998,681	H1202Y	probably benign	Het
Dnah8	T	A	17: 30,765,635	N3102K	probably benign	Het
Dst	A	T	1: 34,116,128	K85M	probably damaging	Het
Ehbp1l1	T	C	19: 5,718,757	I839M	probably benign	Het
Fam184b	T	A	5: 45,537,653	M750L	probably benign	Het
Frem2	T	C	3: 53,572,378	T1965A	probably benign	Het
Ftl1	A	T	7: 45,459,210	D41E	probably benign	Het
Garem2	G	A	5: 30,116,737	W698*	probably null	Het
Glt8d2	T	C	10: 82,652,906	Y283C	probably damaging	Het
Hars	T	C	18: 36,773,590	E109G	possibly damaging	Het
Hspb9	T	C	11: 100,714,210	S121P	probably damaging	Het
Hus1b	A	T	13: 30,947,205	L157Q	probably damaging	Het
Hykk	A	G	9: 54,946,359	M322V	probably benign	Het
Igkv4-61	C	A	6: 69,417,154	A31S	possibly damaging	Het
Il17f	T	A	1: 20,777,907	M116L	probably benign	Het
Kif22	T	C	7: 127,028,932	K9E	possibly damaging	Het
Krt90	T	C	15: 101,559,244	E233G	probably benign	Het
Lipg	T	C	18: 74,957,236	M81V	probably benign	Het
Mocos	C	T	18: 24,701,456	S850L	probably damaging	Het
Mug2	T	A	6: 122,082,754	S1364T	probably damaging	Het
Neb	A	T	2: 52,185,328	N208K	probably benign	Het
Oca2	G	T	7: 56,328,767	R561L	probably benign	Het
Olfm5	A	G	7: 104,154,053	L401P	probably damaging	Het
Olfr109	T	A	17: 37,467,080	Y291*	probably null	Het
Olfr1238	C	A	2: 89,406,522	A186S	possibly damaging	Het
Olfr331	T	C	11: 58,502,340	D72G	probably damaging	Het
Olfr828	G	A	9: 18,815,892	T134M	probably benign	Het
Olfr952	T	A	9: 39,426,891	Y60F	probably damaging	Het
Oxgr1	T	C	14: 120,022,448	N116D	probably damaging	Het
Pcdha11	G	T	18: 37,012,169		probably null	Het
Pi4ka	T	C	16: 17,358,322	I418V	probably benign	Het
Pih1d2	T	C	9: 50,618,609	V62A	probably benign	Het
Pkib	T	A	10: 57,728,138	V46E	probably damaging	Het
Pum1	A	G	4: 130,728,287		probably null	Het
Rbak	G	T	5: 143,176,552	Q19K	possibly damaging	Het
Sema3c	A	G	5: 17,576,961	T32A	probably damaging	Het
Shprh	T	C	10: 11,167,873	W835R	probably damaging	Het
Sis	T	G	3: 72,911,854	K1456N	probably damaging	Het
Slc4a4	A	T	5: 89,179,729	N675I	probably benign	Het
Slc8a3	C	A	12: 81,315,627	M139I	probably damaging	Het
Sorcs3	T	C	19: 48,802,759	F1182S	probably damaging	Het
St8sia2	A	T	7: 73,971,921	I96N	probably damaging	Het
Stx19	T	C	16: 62,822,057	S79P	probably damaging	Het
Tecta	C	T	9: 42,375,267	V698M	probably damaging	Het
Timm22	T	C	11: 76,411,139	S150P	probably damaging	Het
Tjp1	C	T	7: 65,313,205	D995N	possibly damaging	Het
Tmem135	T	A	7: 89,147,794	T365S	probably benign	Het
Tmem174	T	C	13: 98,636,981	T114A	probably benign	Het
Tnc	A	G	4: 64,007,816	I909T	probably benign	Het
Trcg1	A	G	9: 57,241,330	I62V	possibly damaging	Het
Tulp1	A	T	17: 28,356,031	*487K	probably null	Het
Unc79	T	A	12: 103,131,646	V1826E	possibly damaging	Het
Vmn2r13	A	T	5: 109,174,116	N238K	probably damaging	Het
Vmn2r22	T	A	6: 123,637,738	N298Y	probably damaging	Het
Vmn2r23	T	A	6: 123,712,902	F246I	probably damaging	Het
Zfp260	A	T	7: 30,104,810	H45L	possibly damaging	Het
Zfp846	A	T	9: 20,593,720	H292L	possibly 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
R6061:Vps9d1	UTSW	8	123245671	missense	probably damaging	0.99
R6250:Vps9d1	UTSW	8	123248208	critical splice acceptor site	probably null
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

Predicted Primers

PCR Primer
(F):5'- AGAGTCTAACTAGGTCCCCAAGAG -3'
(R):5'- AGCTGACACCACTGGAGAAG -3'

Sequencing Primer
(F):5'- TCCCCAAGAGCGGAGGAAG -3'
(R):5'- CACATATGAGGCCCGGATG -3'

Posted On

2018-05-24