Mutagenetix > Incidental Mutation

Incidental Mutation 'R1813:Vps9d1'

202559

Institutional Source

Beutler Lab

Gene Symbol

Vps9d1

Ensembl Gene

ENSMUSG00000001062

Gene Name

VPS9 domain containing 1

Synonyms

2410004N05Rik, 1300018I17Rik

MMRRC Submission

039841-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1813 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

123969095-123980961 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 123973778 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Leucine at position 335 (R335L)

Ref Sequence

ENSEMBL: ENSMUSP00000113634 (fasta)

Gene Model

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

AlphaFold

Q8C190

Predicted Effect

possibly damaging
Transcript: ENSMUST00000117643
AA Change: R335L

PolyPhen 2 Score 0.795 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000113748
Gene: ENSMUSG00000001062
AA Change: R335L

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: R335L

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000113634
Gene: ENSMUSG00000001062
AA Change: R335L

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: R335L

PolyPhen 2 Score 0.795 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000113575
Gene: ENSMUSG00000001062
AA Change: R335L

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: ENSMUST00000149490

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000211876

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130965

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137569

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130275

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155853

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000181432

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146136

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

Meta Mutation Damage Score

0.1475

Coding Region Coverage

1x: 97.5%
3x: 96.8%
10x: 94.8%
20x: 90.3%

Validation Efficiency

96% (79/82)

Allele List at MGI

Other mutations in this stock

Total: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A2ml1	T	A	6: 128,543,236 (GRCm39)	N595Y	probably benign	Het
Abca6	A	G	11: 110,124,671 (GRCm39)		probably benign	Het
Abo	C	A	2: 26,733,609 (GRCm39)	D199Y	probably damaging	Het
Acvr1c	A	C	2: 58,170,306 (GRCm39)	V277G	probably damaging	Het
Adam23	G	A	1: 63,584,731 (GRCm39)	A380T	probably benign	Het
Art2b	A	G	7: 101,229,236 (GRCm39)	V221A	probably benign	Het
Bcam	A	G	7: 19,500,640 (GRCm39)	S153P	probably damaging	Het
Brip1	T	C	11: 86,077,906 (GRCm39)	H174R	possibly damaging	Het
Ccdc186	T	C	19: 56,788,601 (GRCm39)	D536G	probably benign	Het
Cd109	A	G	9: 78,524,287 (GRCm39)	N67S	probably benign	Het
Cd8a	G	T	6: 71,350,947 (GRCm39)	M137I	possibly damaging	Het
Ces2g	T	C	8: 105,693,569 (GRCm39)	F417L	probably benign	Het
Clec2g	A	G	6: 128,925,660 (GRCm39)	N23S	unknown	Het
Cntnap2	T	C	6: 46,507,567 (GRCm39)	Y61C	probably damaging	Het
Cog3	T	A	14: 75,979,784 (GRCm39)	E182D	probably benign	Het
Dbpht2	A	G	12: 74,342,624 (GRCm39)		noncoding transcript	Het
Dock4	A	T	12: 40,686,227 (GRCm39)	N154I	probably damaging	Het
Dysf	T	G	6: 84,128,906 (GRCm39)	V1422G	possibly damaging	Het
E2f3	T	C	13: 30,104,159 (GRCm39)	D140G	probably damaging	Het
Efcab3	A	G	11: 104,611,514 (GRCm39)	K452R	probably benign	Het
Epb41l2	T	A	10: 25,317,466 (GRCm39)		probably null	Het
Epha2	A	G	4: 141,035,857 (GRCm39)	K98E	possibly damaging	Het
Esyt1	T	C	10: 128,355,487 (GRCm39)	D444G	probably benign	Het
Fam163a	T	C	1: 155,955,787 (GRCm39)	T2A	probably damaging	Het
Foxp2	A	T	6: 15,379,767 (GRCm39)		probably benign	Het
Gcm2	T	C	13: 41,259,367 (GRCm39)	H34R	probably benign	Het
Gipr	A	G	7: 18,897,996 (GRCm39)	S79P	probably benign	Het
Gli3	T	C	13: 15,823,276 (GRCm39)	S333P	probably damaging	Het
Gm10717	T	G	9: 3,026,317 (GRCm39)	F205C	probably damaging	Het
Gzmk	A	G	13: 113,309,427 (GRCm39)	S208P	probably damaging	Het
Htra2	G	T	6: 83,028,583 (GRCm39)	A318D	probably damaging	Het
Itpkc	T	C	7: 26,907,805 (GRCm39)	D633G	probably damaging	Het
Lama1	G	A	17: 68,098,218 (GRCm39)	R1805H	probably benign	Het
Lama4	T	A	10: 38,909,121 (GRCm39)		probably benign	Het
Lama4	T	C	10: 38,936,182 (GRCm39)	V619A	probably damaging	Het
Notch3	T	C	17: 32,362,402 (GRCm39)	T1408A	probably benign	Het
Nwd2	A	G	5: 63,962,753 (GRCm39)	D779G	probably benign	Het
Nxpe4	A	G	9: 48,304,678 (GRCm39)	Y255C	possibly damaging	Het
Obox6	A	T	7: 15,568,770 (GRCm39)	H35Q	possibly damaging	Het
Or2ab1	A	G	11: 58,489,133 (GRCm39)	I304V	probably damaging	Het
Or8b41	T	A	9: 38,055,025 (GRCm39)	I198N	possibly damaging	Het
Pkig	T	A	2: 163,563,147 (GRCm39)	I26N	possibly damaging	Het
Plekhm2	C	T	4: 141,369,750 (GRCm39)	V82M	possibly damaging	Het
Plppr2	G	A	9: 21,859,220 (GRCm39)	A446T	probably damaging	Het
Psme4	T	A	11: 30,754,353 (GRCm39)	F203L	probably benign	Het
Sh3bp1	A	G	15: 78,787,880 (GRCm39)	K137E	probably damaging	Het
Shisa5	T	A	9: 108,885,108 (GRCm39)	I126N	probably damaging	Het
Slc11a1	T	C	1: 74,414,931 (GRCm39)	L21P	probably benign	Het
Slc35f1	C	T	10: 52,809,291 (GRCm39)	P93S	probably damaging	Het
Slc4a4	A	G	5: 89,194,167 (GRCm39)	T172A	probably damaging	Het
Slc9c1	A	T	16: 45,393,710 (GRCm39)	Y551F	probably benign	Het
Spata31	T	C	13: 65,069,612 (GRCm39)	S587P	probably benign	Het
Syna	C	A	5: 134,588,006 (GRCm39)	M314I	probably benign	Het
Taf5l	A	G	8: 124,730,152 (GRCm39)	L144P	probably damaging	Het
Tbccd1	T	C	16: 22,641,271 (GRCm39)	T369A	probably benign	Het
Tnfrsf11b	A	T	15: 54,119,493 (GRCm39)	C160*	probably null	Het
Trim45	A	G	3: 100,830,283 (GRCm39)	N19S	probably benign	Het
Uba2	A	G	7: 33,850,455 (GRCm39)	F364S	probably damaging	Het
Unc50	T	A	1: 37,476,323 (GRCm39)	L161Q	probably damaging	Het
Uso1	A	T	5: 92,348,992 (GRCm39)		probably null	Het
Usp25	A	G	16: 76,911,838 (GRCm39)	I956V	probably benign	Het
Utf1	C	A	7: 139,524,213 (GRCm39)	L143I	probably damaging	Het
Vmn1r158	C	T	7: 22,490,143 (GRCm39)	C22Y	probably damaging	Het
Vmn1r36	T	A	6: 66,693,756 (GRCm39)	M40L	probably benign	Het
Vmn2r43	A	G	7: 8,258,055 (GRCm39)	V386A	possibly damaging	Het
Wasf1	T	A	10: 40,802,585 (GRCm39)	V80D	probably damaging	Het
Wdr72	G	A	9: 74,183,298 (GRCm39)	V1077I	possibly damaging	Het
Wnt8a	A	G	18: 34,675,422 (GRCm39)	M1V	probably null	Het
Zbtb26	A	G	2: 37,326,347 (GRCm39)	S230P	possibly damaging	Het
Zfp335	A	G	2: 164,734,525 (GRCm39)	V1247A	probably damaging	Het
Zfp429	T	C	13: 67,538,505 (GRCm39)	N313S	possibly damaging	Het
Zfp74	A	T	7: 29,634,569 (GRCm39)	C380S	probably damaging	Het
Zfyve21	G	A	12: 111,791,328 (GRCm39)	E134K	probably damaging	Het
Zmynd11	T	C	13: 9,739,616 (GRCm39)	T474A	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
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
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'- ACTGTTCCAGATCCTCAAAGGAG -3'
(R):5'- GCACTTAAGGCCCATCTTGC -3'

Sequencing Primer
(F):5'- TCTGGCAGGTGGGATAAAGCATC -3'
(R):5'- GGCCCATCTTGCCTGCTTTTC -3'

Posted On

2014-06-23