Mutagenetix > Incidental Mutation

Incidental Mutation 'R7431:Vps29'

576460

Institutional Source

Beutler Lab

Gene Symbol

Vps29

Ensembl Gene

ENSMUSG00000029462

Gene Name

VPS29 retromer complex component

Synonyms

PEP11, 2010015D08Rik

MMRRC Submission

045509-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.966) question?

Stock #

R7431 (G1)

Quality Score

198.009

Status

Validated

Chromosome

Chromosomal Location

122492432-122503047 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 122492541 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 2 (V2A)

Ref Sequence

ENSEMBL: ENSMUSP00000123593 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000049009] [ENSMUST00000111729] [ENSMUST00000117263] [ENSMUST00000117868] [ENSMUST00000118765] [ENSMUST00000118830] [ENSMUST00000144268] [ENSMUST00000145821] [ENSMUST00000154686] [ENSMUST00000155671]

AlphaFold

Q9QZ88

Predicted Effect

probably benign
Transcript: ENSMUST00000049009

SMART Domains

Protein: ENSMUSP00000036177
Gene: ENSMUSG00000038569

Domain	Start	End	E-Value	Type
Pfam:Rad9	14	271	1.8e-91	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000111729

SMART Domains

Protein: ENSMUSP00000107358
Gene: ENSMUSG00000029462

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

Predicted Effect

probably benign
Transcript: ENSMUST00000117263

SMART Domains

Protein: ENSMUSP00000113868
Gene: ENSMUSG00000038569

Domain	Start	End	E-Value	Type
Pfam:Rad9	14	271	1.1e-93	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000117868

SMART Domains

Protein: ENSMUSP00000113345
Gene: ENSMUSG00000029462

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

Predicted Effect

probably null
Transcript: ENSMUST00000118765

SMART Domains

Protein: ENSMUSP00000112579
Gene: ENSMUSG00000029462

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

Predicted Effect

probably null
Transcript: ENSMUST00000118830

SMART Domains

Protein: ENSMUSP00000113525
Gene: ENSMUSG00000029462

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

Predicted Effect

probably benign
Transcript: ENSMUST00000144268

SMART Domains

Protein: ENSMUSP00000117334
Gene: ENSMUSG00000038569

Domain	Start	End	E-Value	Type
Pfam:Rad9	1	64	6.7e-17	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000145821
AA Change: V2A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000123593
Gene: ENSMUSG00000029462
AA Change: V2A

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

Predicted Effect

probably benign
Transcript: ENSMUST00000149600

SMART Domains

Protein: ENSMUSP00000120843
Gene: ENSMUSG00000038569

Domain	Start	End	E-Value	Type
Pfam:Rad9	1	85	4.3e-25	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000154686

Predicted Effect

probably null
Transcript: ENSMUST00000155671

SMART Domains

Protein: ENSMUSP00000121020
Gene: ENSMUSG00000029462

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: 99.5%
20x: 98.3%

Validation Efficiency

97% (77/79)

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: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca9	CA	C	11: 110,018,252 (GRCm39)		probably null	Het
Abcf3	G	T	16: 20,377,539 (GRCm39)	R510L	probably benign	Het
Abcg4	T	A	9: 44,185,997 (GRCm39)	I625F	possibly damaging	Het
Adam22	A	T	5: 8,142,818 (GRCm39)	S806T	probably damaging	Het
Adcy4	T	C	14: 56,010,129 (GRCm39)	I718V	probably benign	Het
Adgb	A	T	10: 10,267,699 (GRCm39)		probably null	Het
Aldoart1	T	A	4: 72,769,678 (GRCm39)	K377*	probably null	Het
Apc2	T	A	10: 80,138,017 (GRCm39)	V100E	possibly damaging	Het
Asxl3	T	G	18: 22,650,010 (GRCm39)	D666E	probably damaging	Het
Atg4c	A	T	4: 99,109,632 (GRCm39)	I200F	possibly damaging	Het
Atp1a4	A	G	1: 172,078,474 (GRCm39)	F255L	probably benign	Het
Bod1l	A	C	5: 41,970,463 (GRCm39)		probably null	Het
Cacna2d4	A	T	6: 119,221,237 (GRCm39)	T250S	probably damaging	Het
Ccdc202	A	G	14: 96,119,273 (GRCm39)	H10R	probably benign	Het
Ccng1	G	A	11: 40,644,745 (GRCm39)	R51W	possibly damaging	Het
Chd6	T	C	2: 160,868,248 (GRCm39)	E366G	possibly damaging	Het
Clca4b	A	T	3: 144,616,894 (GRCm39)	S919T	probably benign	Het
Col5a3	T	C	9: 20,682,131 (GRCm39)	*1740W	probably null	Het
Col6a5	A	T	9: 105,805,468 (GRCm39)	I1146K	unknown	Het
Cpxm1	T	C	2: 130,235,966 (GRCm39)	T399A	probably benign	Het
Cpz	T	C	5: 35,668,486 (GRCm39)	T375A	probably benign	Het
Cyp2b13	T	A	7: 25,760,976 (GRCm39)	V11D	probably damaging	Het
Cyp39a1	A	G	17: 43,993,906 (GRCm39)	T189A	probably benign	Het
Desi2	C	T	1: 178,084,007 (GRCm39)	Q52*	probably null	Het
Dhx15	A	G	5: 52,319,953 (GRCm39)	V418A	probably damaging	Het
Dnah3	T	A	7: 119,650,967 (GRCm39)	M978L	probably damaging	Het
Dpagt1	T	A	9: 44,237,384 (GRCm39)	C17*	probably null	Het
Dph5	A	T	3: 115,686,381 (GRCm39)	K52N	possibly damaging	Het
Dpp4	G	T	2: 62,182,582 (GRCm39)	N566K	probably benign	Het
Elavl4	T	C	4: 110,083,830 (GRCm39)	Y94C	probably damaging	Het
Fat2	G	A	11: 55,199,927 (GRCm39)	T1049I	probably damaging	Het
Fat4	T	A	3: 39,063,306 (GRCm39)	Y4421N	possibly damaging	Het
Fcrl2	C	A	3: 87,166,233 (GRCm39)	A181S	probably damaging	Het
Garre1	T	C	7: 33,984,219 (GRCm39)	I135V	possibly damaging	Het
Glg1	G	T	8: 111,887,386 (GRCm39)	N456K	unknown	Het
Gm10228	A	G	16: 88,838,101 (GRCm39)	S68P	unknown	Het
Golga4	G	A	9: 118,388,799 (GRCm39)	E1974K	probably damaging	Het
Heatr9	G	T	11: 83,410,094 (GRCm39)	P49Q	probably damaging	Het
Hmgxb3	A	T	18: 61,280,517 (GRCm39)	V662D	probably damaging	Het
Hs3st4	T	C	7: 123,582,513 (GRCm39)	L37P	probably damaging	Het
Ifi205	A	T	1: 173,855,943 (GRCm39)	M29K	probably benign	Het
Igkv1-35	C	T	6: 69,987,988 (GRCm39)	V103M	probably damaging	Het
Klf13	T	A	7: 63,541,504 (GRCm39)	K208*	probably null	Het
Klhl36	A	G	8: 120,597,121 (GRCm39)	N274S	probably benign	Het
Mosmo	T	A	7: 120,329,873 (GRCm39)	L165I	probably benign	Het
Mtcl1	G	A	17: 66,649,901 (GRCm39)	Q1855*	probably null	Het
Muc16	A	G	9: 18,519,289 (GRCm39)	V208A		Het
Nin	T	G	12: 70,124,997 (GRCm39)	R108S		Het
Odad1	T	G	7: 45,578,670 (GRCm39)	L81R	probably damaging	Het
Or13c7d	T	C	4: 43,770,882 (GRCm39)	N43S	probably damaging	Het
Polr1a	G	A	6: 71,903,643 (GRCm39)	V319I	probably benign	Het
Pramel7	A	G	2: 87,320,282 (GRCm39)	V337A	possibly damaging	Het
Prkar2b	A	T	12: 32,013,150 (GRCm39)		probably null	Het
R3hdm2	T	A	10: 127,294,016 (GRCm39)	M170K	probably benign	Het
Rbm26	A	G	14: 105,354,528 (GRCm39)	I919T	possibly damaging	Het
Rimkla	A	G	4: 119,335,008 (GRCm39)	M125T	probably benign	Het
Sag	T	A	1: 87,749,059 (GRCm39)	F153I	possibly damaging	Het
Sbf2	G	T	7: 109,950,957 (GRCm39)	D1163E	probably damaging	Het
Scgb2b24	T	C	7: 33,438,674 (GRCm39)	I13V	probably benign	Het
Scin	G	A	12: 40,183,921 (GRCm39)	H63Y	probably damaging	Het
Sele	A	G	1: 163,879,189 (GRCm39)	T275A	probably damaging	Het
Slc22a15	T	A	3: 101,805,256 (GRCm39)	T144S	probably benign	Het
Slc8a1	T	A	17: 81,749,092 (GRCm39)	K650I	probably benign	Het
Slc9c1	G	T	16: 45,413,847 (GRCm39)	V992F	probably damaging	Het
Spag16	A	T	1: 69,963,031 (GRCm39)	T393S	unknown	Het
Taf15	G	A	11: 83,395,779 (GRCm39)	D495N	unknown	Het
Tas2r144	T	A	6: 42,192,908 (GRCm39)	I216N	probably damaging	Het
Tbccd1	G	T	16: 22,644,563 (GRCm39)	P271Q	probably benign	Het
Tcf4	C	A	18: 69,480,249 (GRCm39)		probably null	Het
Thap4	A	T	1: 93,678,223 (GRCm39)	S188T	probably benign	Het
Trank1	T	C	9: 111,191,470 (GRCm39)	V493A	probably benign	Het
Trip11	A	G	12: 101,850,278 (GRCm39)	V1262A	possibly damaging	Het
Tspan2	T	A	3: 102,657,107 (GRCm39)	W35R	probably damaging	Het
Usp39	G	T	6: 72,313,251 (GRCm39)	T313N	possibly damaging	Het
Vmn2r83	T	A	10: 79,327,306 (GRCm39)	L638Q	probably damaging	Het
Wrap53	A	G	11: 69,469,313 (GRCm39)	F148L	possibly damaging	Het
Znfx1	T	C	2: 166,897,712 (GRCm39)	Y404C	probably damaging	Het
Zrsr2-ps1	A	G	11: 22,923,580 (GRCm39)	E118G	probably benign	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
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
R8971:Vps29	UTSW	5	122,498,212 (GRCm39)	missense	probably benign	0.38

Predicted Primers

PCR Primer
(F):5'- CACGAGCGATTTCTTGCAGC -3'
(R):5'- TGATGCAGACTGGGTAAGC -3'

Sequencing Primer
(F):5'- ATTTCTTGCAGCGCCGG -3'
(R):5'- ACGACATCGCTCAATGGG -3'

Posted On

2019-10-07