Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL01700:Vps29'

104431

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Vps29

Ensembl Gene

ENSMUSG00000029462

Gene Name

VPS29 retromer complex component

Synonyms

PEP11, 2010015D08Rik

Accession Numbers

Essential gene?

Probably essential (E-score: 0.964) question?

Stock #

IGL01700

Quality Score

Status

Chromosome

Chromosomal Location

122492432-122503047 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 122500930 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 165 (Y165C)

Ref Sequence

ENSEMBL: ENSMUSP00000121020 (fasta)

Gene Model

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

AlphaFold

Q9QZ88

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

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: ENSMUST00000117868

SMART Domains

Protein: ENSMUSP00000113345
Gene: ENSMUSG00000029462

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

Predicted Effect

silent
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 damaging
Transcript: ENSMUST00000118830
AA Change: Y169C

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

SMART Domains

Protein: ENSMUSP00000113525
Gene: ENSMUSG00000029462
AA Change: Y169C

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132785

Predicted Effect

probably benign
Transcript: ENSMUST00000145821

SMART Domains

Protein: ENSMUSP00000123593
Gene: ENSMUSG00000029462

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000155671
AA Change: Y165C

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

SMART Domains

Protein: ENSMUSP00000121020
Gene: ENSMUSG00000029462
AA Change: Y165C

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000199086

Predicted Effect

probably benign
Transcript: ENSMUST00000154686

Coding Region Coverage

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: 37 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca12	T	A	1: 71,319,549 (GRCm39)	M1778L	probably benign	Het
Aldh6a1	C	T	12: 84,486,312 (GRCm39)	C202Y	probably damaging	Het
Ankrd36	A	G	11: 5,582,198 (GRCm39)	T276A	probably benign	Het
Ankrd55	T	C	13: 112,517,702 (GRCm39)	I556T	probably benign	Het
Aqp4	A	G	18: 15,532,922 (GRCm39)	I57T	probably benign	Het
Atp1a1	T	C	3: 101,501,574 (GRCm39)	D43G	possibly damaging	Het
Cyld	G	A	8: 89,433,727 (GRCm39)	R172H	probably damaging	Het
Ear2	A	T	14: 44,340,716 (GRCm39)	R125*	probably null	Het
Efcab9	T	C	11: 32,477,451 (GRCm39)	R24G	probably damaging	Het
F7	C	A	8: 13,078,685 (GRCm39)	Q39K	probably benign	Het
Galntl6	A	T	8: 58,411,494 (GRCm39)		probably benign	Het
Kcnj5	A	G	9: 32,233,925 (GRCm39)	V130A	probably damaging	Het
Magee2	A	G	X: 103,899,574 (GRCm39)	I359T	possibly damaging	Het
Myh1	T	G	11: 67,102,238 (GRCm39)	I843S	probably damaging	Het
Nfat5	T	A	8: 108,065,762 (GRCm39)	M98K	probably damaging	Het
Nrip3	T	A	7: 109,361,074 (GRCm39)	N200I	possibly damaging	Het
Or6c219	A	T	10: 129,781,810 (GRCm39)	N40K	probably damaging	Het
Phkb	A	T	8: 86,744,094 (GRCm39)	Q581L	probably benign	Het
Plxdc2	T	C	2: 16,516,926 (GRCm39)	V69A	probably benign	Het
Pou3f1	G	T	4: 124,552,650 (GRCm39)	W384L	probably damaging	Het
Prrc2a	G	A	17: 35,369,643 (GRCm39)	S1890L	possibly damaging	Het
Psmc1	C	A	12: 100,079,337 (GRCm39)	P27H	probably damaging	Het
Pvr	C	A	7: 19,643,157 (GRCm39)	A359S	probably benign	Het
Rasal1	A	T	5: 120,814,882 (GRCm39)	I711F	probably benign	Het
Ror1	C	T	4: 100,266,968 (GRCm39)	A223V	probably damaging	Het
Slc22a16	A	T	10: 40,479,904 (GRCm39)	I638L	unknown	Het
Slfn10-ps	C	T	11: 82,919,938 (GRCm39)		noncoding transcript	Het
Sptbn4	A	G	7: 27,103,693 (GRCm39)	L1176P	probably damaging	Het
Usp21	A	T	1: 171,110,975 (GRCm39)	F421I	probably damaging	Het
Utp25	G	A	1: 192,800,573 (GRCm39)	P416S	probably damaging	Het
Vmn1r61	T	A	7: 5,614,202 (GRCm39)	R37S	possibly damaging	Het
Vps13a	G	A	19: 16,722,221 (GRCm39)	R364*	probably null	Het
Wdfy4	T	C	14: 32,742,195 (GRCm39)		probably benign	Het
Wdr24	A	G	17: 26,044,802 (GRCm39)	D219G	probably damaging	Het
Xpo1	T	C	11: 23,226,422 (GRCm39)		probably benign	Het
Zfp831	C	A	2: 174,486,711 (GRCm39)	T462K	possibly damaging	Het
Zswim5	T	C	4: 116,843,658 (GRCm39)		probably benign	Het

Other mutations in Vps29

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
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
R8971:Vps29	UTSW	5	122,498,212 (GRCm39)	missense	probably benign	0.38

Posted On

2014-01-21