Mutagenetix > Incidental Mutation

Incidental Mutation 'R8971:Vps29'

683085

Institutional Source

Beutler Lab

Gene Symbol

Vps29

Ensembl Gene

ENSMUSG00000029462

Gene Name

VPS29 retromer complex component

Synonyms

PEP11, 2010015D08Rik

MMRRC Submission

068805-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.966) question?

Stock #

R8971 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

122492432-122503047 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 122498212 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 51 (D51G)

Ref Sequence

ENSEMBL: ENSMUSP00000113525 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000031419] [ENSMUST00000111729] [ENSMUST00000117868] [ENSMUST00000118765] [ENSMUST00000118830] [ENSMUST00000145821] [ENSMUST00000154686] [ENSMUST00000155671]

AlphaFold

Q9QZ88

PDB Structure

Crystal structure of mouse Vps29 complexed with Mn2+ [X-RAY DIFFRACTION]
Crystal structure of mouse Vps29 [X-RAY DIFFRACTION]
Crystal structure of mouse VPS29 complexed with Mn2+ [X-RAY DIFFRACTION]
Crystal structure of mouse VPS29 complexed with Zn2+ [X-RAY DIFFRACTION]

Predicted Effect

probably benign
Transcript: ENSMUST00000031419

SMART Domains

Protein: ENSMUSP00000031419
Gene: ENSMUSG00000029463

Domain	Start	End	E-Value	Type
Pfam:FAM216B	50	160	6e-49	PFAM

Predicted Effect

unknown
Transcript: ENSMUST00000111729
AA Change: T42A

SMART Domains

Protein: ENSMUSP00000107358
Gene: ENSMUSG00000029462
AA Change: T42A

Domain	Start	End	E-Value	Type
low complexity region	26	42	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000117868
AA Change: D47G

PolyPhen 2 Score 0.488 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000113345
Gene: ENSMUSG00000029462
AA Change: D47G

Domain	Start	End	E-Value	Type
Pfam:Metallophos_2	1	143	1.1e-23	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000118765
AA Change: D47G

PolyPhen 2 Score 0.274 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000112579
Gene: ENSMUSG00000029462
AA Change: D47G

Domain	Start	End	E-Value	Type
PDB:1W24\|A	1	65	7e-42	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000118830
AA Change: D51G

PolyPhen 2 Score 0.383 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000113525
Gene: ENSMUSG00000029462
AA Change: D51G

Domain	Start	End	E-Value	Type
Pfam:Metallophos_2	6	162	1.6e-23	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000145821
AA Change: D56G

PolyPhen 2 Score 0.400 (Sensitivity: 0.89; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000123593
Gene: ENSMUSG00000029462
AA Change: D56G

Domain	Start	End	E-Value	Type
Pfam:Metallophos_2	11	124	1e-13	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000154686

Predicted Effect

possibly damaging
Transcript: ENSMUST00000155671
AA Change: D47G

PolyPhen 2 Score 0.488 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000121020
Gene: ENSMUSG00000029462
AA Change: D47G

Domain	Start	End	E-Value	Type
Pfam:Metallophos_2	1	158	3.4e-24	PFAM

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to a group of vacuolar protein sorting (VPS) genes that, when functionally impaired, disrupt the efficient delivery of vacuolar hydrolases. The protein encoded by this gene is a component of a large multimeric complex, termed the retromer complex, which is involved in retrograde transport of proteins from endosomes to the trans-Golgi network. This VPS protein may be involved in the formation of the inner shell of the retromer coat for retrograde vesicles leaving the prevacuolar compartment. Alternative splice variants encoding different isoforms and representing non-protein coding transcripts have been found for this gene. [provided by RefSeq, Aug 2013]

Allele List at MGI

Other mutations in this stock

Total: 86 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9230112D13Rik	T	C	14: 34,236,383 (GRCm39)	H44R	unknown	Het
Acp6	C	T	3: 97,078,961 (GRCm39)	H254Y	probably damaging	Het
Acvrl1	A	G	15: 101,033,404 (GRCm39)	N97S	possibly damaging	Het
Afm	T	A	5: 90,696,675 (GRCm39)	V455E	probably damaging	Het
Ankrd44	G	T	1: 54,692,952 (GRCm39)	D927E	probably benign	Het
Ap2a2	T	C	7: 141,191,258 (GRCm39)	V275A	probably benign	Het
Arfgef2	A	T	2: 166,701,221 (GRCm39)	Q673L	probably damaging	Het
Atp6v0a2	T	C	5: 124,797,061 (GRCm39)	F814L	probably damaging	Het
Axdnd1	G	A	1: 156,219,516 (GRCm39)	A193V		Het
Bicra	T	A	7: 15,721,481 (GRCm39)	I679L	probably benign	Het
Ccm2l	G	A	2: 152,909,756 (GRCm39)	R36H	probably damaging	Het
Cd160	T	A	3: 96,713,102 (GRCm39)	D54V	probably damaging	Het
Cela3a	C	T	4: 137,133,222 (GRCm39)	G50D	probably benign	Het
Cep152	T	A	2: 125,421,770 (GRCm39)	R987*	probably null	Het
Cnnm2	T	C	19: 46,845,362 (GRCm39)	V618A	probably benign	Het
Crim1	G	A	17: 78,653,409 (GRCm39)	R593Q	possibly damaging	Het
Ctsc	A	G	7: 87,959,024 (GRCm39)	S435G	probably benign	Het
Dcbld1	G	T	10: 52,195,958 (GRCm39)	A460S	probably benign	Het
Dcbld2	A	G	16: 58,276,715 (GRCm39)	E502G	probably benign	Het
Dhx30	A	T	9: 109,913,513 (GRCm39)	L1207*	probably null	Het
Dlx2	A	T	2: 71,376,716 (GRCm39)	S7R	possibly damaging	Het
Dmwd	T	A	7: 18,814,973 (GRCm39)	I541N	probably damaging	Het
Dmxl1	T	G	18: 49,997,575 (GRCm39)	L588V	possibly damaging	Het
Dmxl1	C	T	18: 50,026,741 (GRCm39)	P1950S	probably damaging	Het
Dnhd1	T	A	7: 105,358,528 (GRCm39)	L3339*	probably null	Het
Elovl1	C	A	4: 118,288,709 (GRCm39)	P160Q	probably damaging	Het
Epg5	T	A	18: 78,022,434 (GRCm39)	L1059Q	probably damaging	Het
Fam149b	C	T	14: 20,402,777 (GRCm39)	S53F	probably benign	Het
Fat1	T	A	8: 45,495,331 (GRCm39)	C4140S	probably damaging	Het
Gria2	C	T	3: 80,615,200 (GRCm39)	V427I	probably damaging	Het
H2al2a	C	A	2: 18,001,537 (GRCm39)	A50S	probably damaging	Het
Hspbp1	T	C	7: 4,684,858 (GRCm39)	M132V	possibly damaging	Het
Igsf9	C	T	1: 172,312,033 (GRCm39)		probably benign	Het
Jup	C	T	11: 100,270,391 (GRCm39)	C372Y	probably damaging	Het
Katnb1	G	A	8: 95,822,987 (GRCm39)	R394Q	probably damaging	Het
Kif1b	A	T	4: 149,332,273 (GRCm39)	D553E	probably damaging	Het
Kif3a	T	A	11: 53,474,189 (GRCm39)	L251Q	probably damaging	Het
Klb	T	A	5: 65,533,026 (GRCm39)	I445K	probably damaging	Het
Klhl29	T	A	12: 5,190,710 (GRCm39)		probably null	Het
Lipf	A	G	19: 33,942,273 (GRCm39)	K68E	probably benign	Het
Lnx2	T	A	5: 146,970,236 (GRCm39)	I169L	probably benign	Het
Lrba	A	C	3: 86,522,388 (GRCm39)	I2223L	probably benign	Het
Lrp1	C	T	10: 127,391,896 (GRCm39)	D2890N	possibly damaging	Het
Lrp1b	T	C	2: 41,325,640 (GRCm39)	T926A		Het
Lrrc37a	T	A	11: 103,391,490 (GRCm39)	I1312F	probably benign	Het
Lrrc71	T	C	3: 87,647,153 (GRCm39)	H477R	possibly damaging	Het
Lrrc8e	T	C	8: 4,284,141 (GRCm39)	V122A	probably damaging	Het
Lsm14b	T	C	2: 179,667,107 (GRCm39)		probably null	Het
Magel2	A	C	7: 62,029,999 (GRCm39)	I968L	unknown	Het
Mapkbp1	T	C	2: 119,850,050 (GRCm39)	V771A	probably benign	Het
Mtmr4	T	C	11: 87,493,626 (GRCm39)	S295P	probably benign	Het
Nanos3	T	A	8: 84,902,815 (GRCm39)	T116S	probably benign	Het
Nectin3	T	C	16: 46,269,265 (GRCm39)	D379G	probably benign	Het
Nelfa	T	C	5: 34,093,539 (GRCm39)	H14R	possibly damaging	Het
Nnt	A	G	13: 119,502,967 (GRCm39)	W593R	unknown	Het
Nudt2	A	T	4: 41,477,575 (GRCm39)	M19L	probably benign	Het
Or4c115	T	A	2: 88,927,891 (GRCm39)	K127*	probably null	Het
Or52p1	A	T	7: 104,267,467 (GRCm39)	T194S	probably damaging	Het
Or5m13b	T	C	2: 85,754,328 (GRCm39)	S239P	probably damaging	Het
Or5w22	T	A	2: 87,362,580 (GRCm39)	C68S	probably benign	Het
Or6f1	T	A	7: 85,970,369 (GRCm39)	I264F	possibly damaging	Het
Palld	A	T	8: 61,969,735 (GRCm39)	D1196E	unknown	Het
Parl	A	G	16: 20,116,909 (GRCm39)	L96P	probably damaging	Het
Pip4k2a	T	C	2: 18,852,367 (GRCm39)	D305G	probably benign	Het
Pkhd1l1	T	C	15: 44,392,915 (GRCm39)	V1750A	possibly damaging	Het
Prkdc	A	G	16: 15,493,229 (GRCm39)	E712G	probably null	Het
Rasgrf2	T	C	13: 92,158,225 (GRCm39)	E532G	possibly damaging	Het
Rbp3	T	A	14: 33,677,792 (GRCm39)	L580Q	probably damaging	Het
Ribc2	G	T	15: 85,016,337 (GRCm39)		probably benign	Het
Rmnd5b	T	C	11: 51,515,322 (GRCm39)	S315G	probably benign	Het
Rp1l1	T	A	14: 64,259,445 (GRCm39)	V29E	probably damaging	Het
Sclt1	T	C	3: 41,681,541 (GRCm39)	T93A	probably benign	Het
Shroom1	T	A	11: 53,355,994 (GRCm39)	L348H	probably damaging	Het
Slc13a1	T	C	6: 24,090,785 (GRCm39)	K545E	probably benign	Het
Slc20a2	C	T	8: 23,030,396 (GRCm39)	P151S	probably damaging	Het
Slc22a4	T	C	11: 53,879,718 (GRCm39)	Y447C	probably damaging	Het
Slu7	C	A	11: 43,333,480 (GRCm39)	Q367K	probably benign	Het
Spen	T	C	4: 141,201,889 (GRCm39)	N2246S	possibly damaging	Het
Tac4	T	G	11: 95,156,045 (GRCm39)	I42S	possibly damaging	Het
Tmem87a	A	G	2: 120,190,541 (GRCm39)	V530A		Het
Tnrc6c	T	C	11: 117,640,089 (GRCm39)	I1208T	possibly damaging	Het
Vmn1r230	C	T	17: 21,067,321 (GRCm39)	T170I	possibly damaging	Het
Washc2	T	C	6: 116,231,399 (GRCm39)	L874P	probably damaging	Het
Wdr5b	T	C	16: 35,861,926 (GRCm39)	L15P	probably benign	Het
Zscan20	T	A	4: 128,479,847 (GRCm39)	Q881H	probably damaging	Het
Zscan20	T	G	4: 128,479,848 (GRCm39)	Q881P	probably damaging	Het

Other mutations in Vps29

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01700:Vps29	APN	5	122,500,930 (GRCm39)	missense	probably damaging	1.00
IGL02627:Vps29	APN	5	122,500,908 (GRCm39)	missense	probably benign	0.00
IGL02716:Vps29	APN	5	122,500,129 (GRCm39)	missense	probably benign	0.20
R4807:Vps29	UTSW	5	122,500,951 (GRCm39)	missense	probably damaging	1.00
R5619:Vps29	UTSW	5	122,492,511 (GRCm39)	utr 5 prime	probably benign
R7431:Vps29	UTSW	5	122,492,541 (GRCm39)	missense	probably benign
R7866:Vps29	UTSW	5	122,500,180 (GRCm39)	missense	possibly damaging	0.91
R8167:Vps29	UTSW	5	122,500,877 (GRCm39)	missense	possibly damaging	0.95

Predicted Primers

PCR Primer
(F):5'- ACTGTCTGAGTGACTTCTGCTC -3'
(R):5'- ACGTTTTCAATGGGGCAGG -3'

Sequencing Primer
(F):5'- GACGTCATGTCTAACGCTGTG -3'
(R):5'- TTTCAATGGGGCAGGGGAGG -3'

Posted On

2021-10-11