Mutagenetix > Incidental Mutation

Incidental Mutation 'R2146:Vps51'

233872

Institutional Source

Beutler Lab

Gene Symbol

Vps51

Ensembl Gene

ENSMUSG00000024797

Gene Name

VPS51 GARP complex subunit

Synonyms

MMRRC Submission

040149-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2146 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

6067842-6080324 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 6068134 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 777 (V777A)

Ref Sequence

ENSEMBL: ENSMUSP00000123994 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025711] [ENSMUST00000025713] [ENSMUST00000113543] [ENSMUST00000159084] [ENSMUST00000159832] [ENSMUST00000160028] [ENSMUST00000160233] [ENSMUST00000161718] [ENSMUST00000161090] [ENSMUST00000162575] [ENSMUST00000162810] [ENSMUST00000161528]

AlphaFold

Q3UVL4

Predicted Effect

probably benign
Transcript: ENSMUST00000025711
AA Change: V777A

PolyPhen 2 Score 0.254 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000025711
Gene: ENSMUSG00000024799
AA Change: V777A

Domain	Start	End	E-Value	Type
low complexity region	2	25	N/A	INTRINSIC
Pfam:COG2	56	191	2.6e-10	PFAM
Pfam:DUF2450	62	250	2.3e-14	PFAM
Pfam:Vps51	63	149	1.1e-26	PFAM
Pfam:Dor1	75	246	1.8e-19	PFAM
Pfam:Zw10	83	291	2.2e-8	PFAM
Pfam:Sec5	101	275	6.5e-24	PFAM
low complexity region	377	391	N/A	INTRINSIC
low complexity region	523	532	N/A	INTRINSIC
low complexity region	743	758	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000025713

SMART Domains

Protein: ENSMUSP00000025713
Gene: ENSMUSG00000024799

Domain	Start	End	E-Value	Type
Pfam:ERG4_ERG24	7	418	1.6e-141	PFAM
Pfam:DUF1295	250	409	9.4e-9	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000113543

SMART Domains

Protein: ENSMUSP00000109171
Gene: ENSMUSG00000024799

Domain	Start	End	E-Value	Type
Pfam:ERG4_ERG24	7	373	9.9e-112	PFAM
Pfam:DUF1295	249	396	2.6e-8	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000159084

SMART Domains

Protein: ENSMUSP00000124868
Gene: ENSMUSG00000024799

Domain	Start	End	E-Value	Type
Pfam:ERG4_ERG24	7	300	6.4e-75	PFAM
Pfam:ERG4_ERG24	292	391	2.2e-48	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000159211

Predicted Effect

probably benign
Transcript: ENSMUST00000159475

Predicted Effect

probably benign
Transcript: ENSMUST00000159832
AA Change: V777A

PolyPhen 2 Score 0.254 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000123994
Gene: ENSMUSG00000024797
AA Change: V777A

Domain	Start	End	E-Value	Type
low complexity region	2	25	N/A	INTRINSIC
Pfam:COG2	56	191	2e-10	PFAM
Pfam:DUF2450	62	250	1.9e-14	PFAM
Pfam:Vps51	63	149	8.3e-27	PFAM
Pfam:Dor1	75	246	1.8e-19	PFAM
Pfam:Sec5	101	275	1.6e-19	PFAM
low complexity region	276	292	N/A	INTRINSIC
low complexity region	377	391	N/A	INTRINSIC
low complexity region	523	532	N/A	INTRINSIC
low complexity region	743	758	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000159836

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000159869

Predicted Effect

probably benign
Transcript: ENSMUST00000160028

SMART Domains

Protein: ENSMUSP00000124847
Gene: ENSMUSG00000024799

Domain	Start	End	E-Value	Type
transmembrane domain	7	29	N/A	INTRINSIC
transmembrane domain	39	61	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000160233

SMART Domains

Protein: ENSMUSP00000124842
Gene: ENSMUSG00000024797

Domain	Start	End	E-Value	Type
low complexity region	2	25	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160324

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160354

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160519

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162721

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162549

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161222

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161634

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160417

Predicted Effect

probably benign
Transcript: ENSMUST00000161718

SMART Domains

Protein: ENSMUSP00000124283
Gene: ENSMUSG00000024799

Domain	Start	End	E-Value	Type
Pfam:ERG4_ERG24	1	197	5.7e-86	PFAM
Pfam:DUF1295	46	185	1e-8	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000161090

SMART Domains

Protein: ENSMUSP00000125543
Gene: ENSMUSG00000024799

Domain	Start	End	E-Value	Type
transmembrane domain	13	35	N/A	INTRINSIC
transmembrane domain	57	79	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000162575

SMART Domains

Protein: ENSMUSP00000125586
Gene: ENSMUSG00000024799

Domain	Start	End	E-Value	Type
transmembrane domain	13	35	N/A	INTRINSIC
Pfam:ERG4_ERG24	51	229	5.5e-59	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000162810

SMART Domains

Protein: ENSMUSP00000124825
Gene: ENSMUSG00000024799

Domain	Start	End	E-Value	Type
Pfam:ERG4_ERG24	9	124	6.9e-34	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000161528

SMART Domains

Protein: ENSMUSP00000123989
Gene: ENSMUSG00000024799

Domain	Start	End	E-Value	Type
Pfam:ERG4_ERG24	7	109	5.3e-9	PFAM

Meta Mutation Damage Score

0.1300

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.4%

Validation Efficiency

99% (84/85)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the vacuolar protein sorting-associated protein 51 family. The encoded protein is a component of the Golgi-associated retrograde protein complex which acts as a tethering factor for carriers in retrograde transport from the early and late endosomes to the trans-Golgi network. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]

Allele List at MGI

Other mutations in this stock

Total: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700013D24Rik	A	T	6: 124,347,844 (GRCm38)		probably null	Het
9530002B09Rik	T	A	4: 122,689,405 (GRCm38)	C13*	probably null	Het
Abca12	C	A	1: 71,263,488 (GRCm38)	V2191L	probably benign	Het
Adamts18	G	C	8: 113,845,003 (GRCm38)	A116G	possibly damaging	Het
Anxa2	TCCC	TCC	9: 69,489,754 (GRCm38)		probably null	Het
Arfgef1	C	T	1: 10,199,878 (GRCm38)	A349T	probably benign	Het
Arhgap6	A	G	X: 168,796,500 (GRCm38)	T94A	probably benign	Het
Arhgef5	T	C	6: 43,283,318 (GRCm38)	S1413P	probably damaging	Het
Atg4c	C	A	4: 99,221,226 (GRCm38)	N143K	possibly damaging	Het
C1qtnf12	A	G	4: 155,966,465 (GRCm38)	N297S	probably benign	Het
Cadps2	G	T	6: 23,838,999 (GRCm38)		probably benign	Het
Ccdc185	G	T	1: 182,747,520 (GRCm38)	H535N	possibly damaging	Het
Ccdc57	A	G	11: 120,885,225 (GRCm38)		probably benign	Het
Cd163	A	G	6: 124,309,208 (GRCm38)	H239R	probably damaging	Het
Ceacam2	G	T	7: 25,527,943 (GRCm38)	C166*	probably null	Het
Ces5a	T	A	8: 93,534,699 (GRCm38)	E33D	probably benign	Het
Chl1	T	C	6: 103,715,401 (GRCm38)		probably null	Het
Chsy3	G	A	18: 59,176,472 (GRCm38)	V266I	probably benign	Het
Cpa5	G	T	6: 30,626,822 (GRCm38)	R251L	probably damaging	Het
Cps1	A	C	1: 67,152,379 (GRCm38)		probably benign	Het
Csmd3	CCTTTGCGCTT	CCTT	15: 47,741,236 (GRCm38)		probably null	Het
Cstf1	T	C	2: 172,375,763 (GRCm38)	Y99H	probably damaging	Het
Cyp2j11	G	A	4: 96,316,358 (GRCm38)	T317I	probably damaging	Het
Dcaf8l	T	C	X: 89,406,277 (GRCm38)	D82G	possibly damaging	Het
Dennd3	A	T	15: 73,555,060 (GRCm38)	H762L	probably benign	Het
Dennd3	C	T	15: 73,523,496 (GRCm38)	T146M	probably damaging	Het
Dnah2	T	C	11: 69,515,761 (GRCm38)	M552V	probably benign	Het
Dnajc22	T	C	15: 99,104,383 (GRCm38)	V303A	probably benign	Het
Dtx2	T	G	5: 136,030,610 (GRCm38)	L458R	probably benign	Het
Fat3	A	T	9: 15,990,512 (GRCm38)	F3072L	probably benign	Het
Fgf5	T	C	5: 98,275,550 (GRCm38)	*265R	probably null	Het
Fndc11	A	G	2: 181,222,125 (GRCm38)	E241G	probably damaging	Het
Glb1	T	C	9: 114,450,648 (GRCm38)	Y375H	probably damaging	Het
Gm4922	T	G	10: 18,783,516 (GRCm38)	Q486P	probably benign	Het
Gm5786	A	T	12: 59,081,298 (GRCm38)		noncoding transcript	Het
Hepacam2	A	T	6: 3,463,378 (GRCm38)		probably benign	Het
Ints9	G	A	14: 64,986,343 (GRCm38)	G89R	possibly damaging	Het
Iqcm	T	A	8: 75,888,613 (GRCm38)	W441R	probably damaging	Het
Itga10	G	T	3: 96,653,723 (GRCm38)	G635W	probably damaging	Het
Itga10	T	C	3: 96,651,492 (GRCm38)	L382P	possibly damaging	Het
Kbtbd2	A	G	6: 56,779,090 (GRCm38)	Y554H	probably damaging	Het
Kif1b	T	C	4: 149,184,309 (GRCm38)	K1649R	probably damaging	Het
L1cam	A	T	X: 73,861,141 (GRCm38)	F536Y	probably damaging	Het
Magee1	A	T	X: 105,122,958 (GRCm38)	D783V	probably damaging	Het
Marveld3	A	T	8: 109,959,802 (GRCm38)	V144E	probably benign	Het
Mcam	T	C	9: 44,136,635 (GRCm38)	V59A	probably damaging	Het
Mdga2	C	T	12: 66,868,741 (GRCm38)	E47K	probably damaging	Het
Metrn	T	A	17: 25,796,627 (GRCm38)	E38V	probably damaging	Het
Mfrp	T	C	9: 44,103,718 (GRCm38)	L314P	probably benign	Het
Mgat4f	T	A	1: 134,390,513 (GRCm38)	M341K	probably damaging	Het
Mideas	G	T	12: 84,173,035 (GRCm38)	P382T	probably damaging	Het
Mospd2	A	G	X: 164,956,477 (GRCm38)		probably null	Het
Mycbp2	G	A	14: 103,155,922 (GRCm38)	H3068Y	probably damaging	Het
Myh6	C	T	14: 54,953,771 (GRCm38)	R871H	probably damaging	Het
Nup214	C	T	2: 32,034,466 (GRCm38)	S1669F	probably damaging	Het
Or13c7b	A	G	4: 43,821,178 (GRCm38)	F61S	probably damaging	Het
Or5b111	T	C	19: 13,314,121 (GRCm38)	T55A	probably benign	Het
Or8i2	T	A	2: 87,021,665 (GRCm38)	N293I	probably damaging	Het
Parvb	A	G	15: 84,232,168 (GRCm38)	K33E	possibly damaging	Het
Pdcd11	A	G	19: 47,104,752 (GRCm38)	M490V	probably benign	Het
Pkd2	A	C	5: 104,455,590 (GRCm38)		probably benign	Het
Reps1	T	A	10: 18,093,313 (GRCm38)	D206E	probably benign	Het
Rimkla	T	A	4: 119,474,582 (GRCm38)	M140L	possibly damaging	Het
Rnf13	T	G	3: 57,802,486 (GRCm38)	I150S	probably null	Het
Rxfp4	C	T	3: 88,652,893 (GRCm38)	A84T	probably damaging	Het
Serpinb8	T	A	1: 107,605,927 (GRCm38)	D237E	probably benign	Het
Sgo2b	T	G	8: 63,928,023 (GRCm38)	T592P	probably benign	Het
Slc35d1	A	T	4: 103,205,152 (GRCm38)	I228N	probably damaging	Het
Slc39a1	T	G	3: 90,249,450 (GRCm38)	H104Q	probably benign	Het
Slc6a6	T	C	6: 91,735,180 (GRCm38)	V230A	probably benign	Het
Slc9a3	A	G	13: 74,121,603 (GRCm38)	E30G	probably benign	Het
Slc9c1	A	G	16: 45,593,464 (GRCm38)	Y985C	probably benign	Het
Supt6	A	G	11: 78,230,932 (GRCm38)	F298S	probably damaging	Het
Tada2a	T	C	11: 84,079,629 (GRCm38)	D432G	probably damaging	Het
Thoc2l	T	C	5: 104,518,991 (GRCm38)	F460L	probably benign	Het
Tmem131	C	A	1: 36,812,609 (GRCm38)	V938L	probably benign	Het
Tnpo3	A	G	6: 29,589,036 (GRCm38)	V105A	probably benign	Het
Ttc7	T	C	17: 87,346,707 (GRCm38)		probably benign	Het
Ttn	T	C	2: 76,897,188 (GRCm38)		probably benign	Het
Usp16	T	C	16: 87,473,187 (GRCm38)		probably null	Het
Usp36	A	G	11: 118,268,665 (GRCm38)	L486S	probably benign	Het
Uty	T	C	Y: 1,239,816 (GRCm38)	I72V	probably benign	Het
Zfp160	A	G	17: 21,026,982 (GRCm38)	K598R	probably benign	Het
Zfp39	T	C	11: 58,890,332 (GRCm38)	N535D	probably benign	Het
Zfp804a	A	G	2: 82,258,664 (GRCm38)	T946A	probably benign	Het

Other mutations in Vps51

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL03095:Vps51	APN	19	6,070,048 (GRCm38)	missense	probably damaging	1.00
R0238:Vps51	UTSW	19	6,071,437 (GRCm38)	nonsense	probably null
R0238:Vps51	UTSW	19	6,071,437 (GRCm38)	nonsense	probably null
R0239:Vps51	UTSW	19	6,071,437 (GRCm38)	nonsense	probably null
R0239:Vps51	UTSW	19	6,071,437 (GRCm38)	nonsense	probably null
R1533:Vps51	UTSW	19	6,071,467 (GRCm38)	missense	probably benign	0.04
R1909:Vps51	UTSW	19	6,069,469 (GRCm38)	missense	probably benign	0.03
R2022:Vps51	UTSW	19	6,071,582 (GRCm38)	missense	probably benign	0.02
R2148:Vps51	UTSW	19	6,068,134 (GRCm38)	missense	probably benign	0.25
R2149:Vps51	UTSW	19	6,068,134 (GRCm38)	missense	probably benign	0.25
R2901:Vps51	UTSW	19	6,076,438 (GRCm38)	missense	probably damaging	0.99
R3717:Vps51	UTSW	19	6,077,168 (GRCm38)	utr 3 prime	probably benign
R3769:Vps51	UTSW	19	6,076,348 (GRCm38)	missense	possibly damaging	0.54
R5192:Vps51	UTSW	19	6,070,467 (GRCm38)	missense	possibly damaging	0.88
R5210:Vps51	UTSW	19	6,071,033 (GRCm38)	missense	probably benign	0.00
R5256:Vps51	UTSW	19	6,070,488 (GRCm38)	missense	probably benign	0.00
R5260:Vps51	UTSW	19	6,071,033 (GRCm38)	missense	probably benign	0.00
R5261:Vps51	UTSW	19	6,071,033 (GRCm38)	missense	probably benign	0.00
R5274:Vps51	UTSW	19	6,071,033 (GRCm38)	missense	probably benign	0.00
R5294:Vps51	UTSW	19	6,071,033 (GRCm38)	missense	probably benign	0.00
R5295:Vps51	UTSW	19	6,071,033 (GRCm38)	missense	probably benign	0.00
R5389:Vps51	UTSW	19	6,071,033 (GRCm38)	missense	probably benign	0.00
R5391:Vps51	UTSW	19	6,071,033 (GRCm38)	missense	probably benign	0.00
R5392:Vps51	UTSW	19	6,071,033 (GRCm38)	missense	probably benign	0.00
R5393:Vps51	UTSW	19	6,071,033 (GRCm38)	missense	probably benign	0.00
R5421:Vps51	UTSW	19	6,071,033 (GRCm38)	missense	probably benign	0.00
R5422:Vps51	UTSW	19	6,071,033 (GRCm38)	missense	probably benign	0.00
R5497:Vps51	UTSW	19	6,071,033 (GRCm38)	missense	probably benign	0.00
R5498:Vps51	UTSW	19	6,071,033 (GRCm38)	missense	probably benign	0.00
R5499:Vps51	UTSW	19	6,071,033 (GRCm38)	missense	probably benign	0.00
R5671:Vps51	UTSW	19	6,068,194 (GRCm38)	missense	probably benign	0.18
R5963:Vps51	UTSW	19	6,068,290 (GRCm38)	missense	probably damaging	1.00
R5989:Vps51	UTSW	19	6,076,372 (GRCm38)	missense	probably damaging	0.96
R6427:Vps51	UTSW	19	6,070,917 (GRCm38)	missense	possibly damaging	0.77
R7247:Vps51	UTSW	19	6,077,389 (GRCm38)	utr 3 prime	probably benign
R9344:Vps51	UTSW	19	6,076,315 (GRCm38)	missense	unknown

Predicted Primers

PCR Primer
(F):5'- AAGCTTCGGCACTGAAACCC -3'
(R):5'- GATCAGCTTGAAGACACTACTGG -3'

Sequencing Primer
(F):5'- GCACTGAAACCCAACCCGG -3'
(R):5'- CTACTGGAGTGTGTGCGCCTAC -3'

Posted On

2014-10-01