Mutagenetix > Incidental Mutation

Incidental Mutation 'R5963:Vps51'

471914

Institutional Source

Beutler Lab

Gene Symbol

Vps51

Ensembl Gene

ENSMUSG00000024797

Gene Name

VPS51 GARP complex subunit

Synonyms

MMRRC Submission

044148-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R5963 (G1)

Quality Score

216

Status

Validated

Chromosome

Chromosomal Location

6067842-6080324 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 6068290 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 725 (L725P)

Ref Sequence

ENSEMBL: ENSMUSP00000123994 (fasta)

Gene Model

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

AlphaFold

Q3UVL4

Predicted Effect

probably damaging
Transcript: ENSMUST00000025711
AA Change: L725P

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

SMART Domains

Protein: ENSMUSP00000025711
Gene: ENSMUSG00000024799
AA Change: L725P

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

unknown
Transcript: ENSMUST00000159475
AA Change: L95P

Predicted Effect

probably damaging
Transcript: ENSMUST00000159832
AA Change: L725P

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

SMART Domains

Protein: ENSMUSP00000123994
Gene: ENSMUSG00000024797
AA Change: L725P

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: ENSMUST00000160417

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160354

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160519

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162721

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161634

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162549

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161222

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

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: 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: 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: 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

Meta Mutation Damage Score

0.9473

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.7%
20x: 92.5%

Validation Efficiency

99% (68/69)

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: 55 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Alg8	A	G	7: 97,379,830	K131E	probably benign	Het
Ank3	T	A	10: 69,987,226	L575*	probably null	Het
Aqr	T	C	2: 114,126,961	T819A	probably damaging	Het
Bbs2	A	T	8: 94,081,031	S407T	probably benign	Het
Bmper	T	A	9: 23,375,593	C272S	probably benign	Het
Btbd9	C	T	17: 30,334,218		probably null	Het
C5ar1	A	G	7: 16,248,822	V91A	possibly damaging	Het
Ccdc138	A	G	10: 58,575,757	H649R	possibly damaging	Het
Cfap43	A	T	19: 47,745,574	V1451E	probably benign	Het
Cfap46	T	A	7: 139,651,595	M901L	probably damaging	Het
Cherp	G	T	8: 72,461,535		probably benign	Het
D430041D05Rik	C	T	2: 104,248,285	V1229I	possibly damaging	Het
Fat4	A	C	3: 39,010,547	D4884A	probably damaging	Het
Fcrl5	T	C	3: 87,444,173	F243L	probably damaging	Het
Garem1	T	A	18: 21,129,430	I776F	probably benign	Het
Gpr87	T	A	3: 59,179,269	R272*	probably null	Het
Gsdmc	A	T	15: 63,780,116		probably null	Het
Hydin	T	A	8: 110,494,294	F1441I	possibly damaging	Het
Ints11	T	A	4: 155,872,912	C63*	probably null	Het
Kdm4b	A	T	17: 56,399,732	T908S	probably damaging	Het
Lipn	A	G	19: 34,081,300	D304G	probably damaging	Het
Man2a1	T	G	17: 64,675,122	N544K	probably benign	Het
Mapkapk5	G	T	5: 121,538,481	H66N	probably damaging	Het
Mog	G	A	17: 37,012,348	R233*	probably null	Het
Mrps24	A	T	11: 5,707,481		probably benign	Het
Nom1	T	C	5: 29,437,770	L423P	probably damaging	Het
Olfr65	T	A	7: 103,906,961	V174E	probably benign	Het
Pcdha1	T	A	18: 36,931,171	V296E	probably damaging	Het
Pdcd2	G	T	17: 15,526,395	H167Q	probably damaging	Het
Pdcd2	T	C	17: 15,526,394	K168E	possibly damaging	Het
Pla2g12b	T	A	10: 59,403,958	V63D	probably damaging	Het
Pnn	C	T	12: 59,067,831	R56*	probably null	Het
Primpol	T	A	8: 46,593,580	E227V	possibly damaging	Het
Rad54l	A	T	4: 116,110,387	W233R	probably damaging	Het
Rims2	A	T	15: 39,437,182	D103V	probably damaging	Het
Rttn	T	C	18: 89,073,695	S1511P	probably benign	Het
Sept5	T	C	16: 18,624,212		probably null	Het
Simc1	T	A	13: 54,525,819	I660K	possibly damaging	Het
Slc15a5	A	G	6: 138,079,693	L75P	probably damaging	Het
Slc9a2	A	G	1: 40,682,036	S55G	possibly damaging	Het
Slit3	C	T	11: 35,700,236	R1292C	probably damaging	Het
Slitrk3	A	G	3: 73,050,713	V242A	probably benign	Het
St14	A	T	9: 31,106,557		probably benign	Het
Tnnt2	T	C	1: 135,843,862		probably benign	Het
Traf5	G	A	1: 192,000,016	T288I	probably benign	Het
Trerf1	C	T	17: 47,314,337		noncoding transcript	Het
Vegfc	A	G	8: 54,181,284	N333D	probably benign	Het
Vmn1r65	T	A	7: 6,008,609	I209F	probably damaging	Het
Vps8	T	C	16: 21,470,121	I408T	possibly damaging	Het
Wdr72	T	C	9: 74,145,028	Y114H	probably damaging	Het
Ybx2	A	G	11: 69,941,092	E164G	probably damaging	Het
Zcchc14	A	T	8: 121,628,623		probably benign	Het
Zfp383	A	G	7: 29,915,678	T453A	possibly damaging	Het
Zfp84	G	T	7: 29,776,953	G357C	probably damaging	Het
Zmynd11	G	T	13: 9,695,895		probably benign	Het

Other mutations in Vps51

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL03095:Vps51	APN	19	6070048	missense	probably damaging	1.00
R0238:Vps51	UTSW	19	6071437	nonsense	probably null
R0238:Vps51	UTSW	19	6071437	nonsense	probably null
R0239:Vps51	UTSW	19	6071437	nonsense	probably null
R0239:Vps51	UTSW	19	6071437	nonsense	probably null
R1533:Vps51	UTSW	19	6071467	missense	probably benign	0.04
R1909:Vps51	UTSW	19	6069469	missense	probably benign	0.03
R2022:Vps51	UTSW	19	6071582	missense	probably benign	0.02
R2146:Vps51	UTSW	19	6068134	missense	probably benign	0.25
R2148:Vps51	UTSW	19	6068134	missense	probably benign	0.25
R2149:Vps51	UTSW	19	6068134	missense	probably benign	0.25
R2901:Vps51	UTSW	19	6076438	missense	probably damaging	0.99
R3717:Vps51	UTSW	19	6077168	utr 3 prime	probably benign
R3769:Vps51	UTSW	19	6076348	missense	possibly damaging	0.54
R5192:Vps51	UTSW	19	6070467	missense	possibly damaging	0.88
R5210:Vps51	UTSW	19	6071033	missense	probably benign	0.00
R5256:Vps51	UTSW	19	6070488	missense	probably benign	0.00
R5260:Vps51	UTSW	19	6071033	missense	probably benign	0.00
R5261:Vps51	UTSW	19	6071033	missense	probably benign	0.00
R5274:Vps51	UTSW	19	6071033	missense	probably benign	0.00
R5294:Vps51	UTSW	19	6071033	missense	probably benign	0.00
R5295:Vps51	UTSW	19	6071033	missense	probably benign	0.00
R5389:Vps51	UTSW	19	6071033	missense	probably benign	0.00
R5391:Vps51	UTSW	19	6071033	missense	probably benign	0.00
R5392:Vps51	UTSW	19	6071033	missense	probably benign	0.00
R5393:Vps51	UTSW	19	6071033	missense	probably benign	0.00
R5421:Vps51	UTSW	19	6071033	missense	probably benign	0.00
R5422:Vps51	UTSW	19	6071033	missense	probably benign	0.00
R5497:Vps51	UTSW	19	6071033	missense	probably benign	0.00
R5498:Vps51	UTSW	19	6071033	missense	probably benign	0.00
R5499:Vps51	UTSW	19	6071033	missense	probably benign	0.00
R5671:Vps51	UTSW	19	6068194	missense	probably benign	0.18
R5989:Vps51	UTSW	19	6076372	missense	probably damaging	0.96
R6427:Vps51	UTSW	19	6070917	missense	possibly damaging	0.77
R7247:Vps51	UTSW	19	6077389	utr 3 prime	probably benign
R9344:Vps51	UTSW	19	6076315	missense	unknown

Predicted Primers

PCR Primer
(F):5'- ATAGGGCTACTACGCGACTC -3'
(R):5'- AGCTGAGCCCTAGAAATTTCTG -3'

Sequencing Primer
(F):5'- GACTCGTTGGCAGATTCTAGCC -3'
(R):5'- GAGCCCTAGAAATTTCTGTCTTTATC -3'

Posted On

2017-03-31