Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02716:Vps29'

304750

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: 0.966) question?

Stock #

IGL02716

Quality Score

Status

Chromosome

Chromosomal Location

122492432-122503047 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 122500129 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 85 (T85A)

Ref Sequence

ENSEMBL: ENSMUSP00000123593 (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
AA Change: T76A

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

SMART Domains

Protein: ENSMUSP00000113345
Gene: ENSMUSG00000029462
AA Change: T76A

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

Predicted Effect

probably benign
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 benign
Transcript: ENSMUST00000118830
AA Change: T80A

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000113525
Gene: ENSMUSG00000029462
AA Change: T80A

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
AA Change: T85A

PolyPhen 2 Score 0.203 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000123593
Gene: ENSMUSG00000029462
AA Change: T85A

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

Predicted Effect

probably benign
Transcript: ENSMUST00000155671
AA Change: T76A

PolyPhen 2 Score 0.027 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000121020
Gene: ENSMUSG00000029462
AA Change: T76A

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: 58 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acsl6	T	C	11: 54,218,102 (GRCm39)	S212P	probably benign	Het
Ago2	C	T	15: 72,983,576 (GRCm39)	R711Q	possibly damaging	Het
Akp3	A	C	1: 87,053,201 (GRCm39)	D91A	probably damaging	Het
Arhgap12	T	A	18: 6,111,857 (GRCm39)	Q169L	possibly damaging	Het
Aspm	A	G	1: 139,407,425 (GRCm39)	Y2104C	probably damaging	Het
Baz2b	G	A	2: 59,792,868 (GRCm39)	S420L	possibly damaging	Het
Cenpo	T	C	12: 4,265,390 (GRCm39)	N210S	possibly damaging	Het
Chadl	T	C	15: 81,580,116 (GRCm39)	N40D	probably damaging	Het
Crebbp	T	C	16: 3,932,742 (GRCm39)	E586G	probably benign	Het
Cts7	T	A	13: 61,504,422 (GRCm39)	Q47L	probably benign	Het
Cyp2c40	C	A	19: 39,795,980 (GRCm39)	D133Y	possibly damaging	Het
Dnah3	A	T	7: 119,536,246 (GRCm39)	M3679K	probably damaging	Het
Dym	T	C	18: 75,419,754 (GRCm39)	Y642H	probably damaging	Het
Efr3b	T	C	12: 4,034,627 (GRCm39)	D65G	probably damaging	Het
Elmo1	T	A	13: 20,633,672 (GRCm39)	F445I	probably damaging	Het
Epdr1	C	T	13: 19,778,740 (GRCm39)	V119M	probably benign	Het
Epha4	G	T	1: 77,357,602 (GRCm39)	R799S	probably damaging	Het
Esyt3	A	T	9: 99,199,277 (GRCm39)	V778E	probably damaging	Het
F10	A	T	8: 13,098,177 (GRCm39)	K127*	probably null	Het
Fcgbp	G	A	7: 27,800,859 (GRCm39)	E1302K	probably damaging	Het
Fer1l4	A	G	2: 155,871,635 (GRCm39)	F1382L	probably damaging	Het
Fhad1	T	C	4: 141,645,642 (GRCm39)	I318V	possibly damaging	Het
Fscn2	A	T	11: 120,257,550 (GRCm39)	T304S	probably benign	Het
Gab1	A	T	8: 81,496,323 (GRCm39)	L659Q	probably damaging	Het
Gm4845	A	C	1: 141,184,576 (GRCm39)		noncoding transcript	Het
Gm572	A	G	4: 148,739,327 (GRCm39)	M52V	probably benign	Het
Hmgcr	T	C	13: 96,796,520 (GRCm39)		probably null	Het
Kcnk5	T	C	14: 20,231,496 (GRCm39)	T9A	probably damaging	Het
Krt87	A	C	15: 101,332,485 (GRCm39)	F243V	possibly damaging	Het
Lyset	A	G	12: 102,711,088 (GRCm39)	T104A	probably benign	Het
Mast1	G	T	8: 85,662,352 (GRCm39)	P52Q	probably damaging	Het
Mcf2l	A	T	8: 13,047,277 (GRCm39)	Q211L	probably benign	Het
Mtrex	T	G	13: 113,019,680 (GRCm39)	D810A	probably benign	Het
Mtus2	C	A	5: 148,173,120 (GRCm39)	P968T	probably benign	Het
Mylk2	T	C	2: 152,764,073 (GRCm39)	*614R	probably null	Het
Myo15b	A	T	11: 115,774,535 (GRCm39)	E2049V	probably benign	Het
Myo6	A	T	9: 80,176,976 (GRCm39)	H581L	probably damaging	Het
Numb	A	T	12: 83,847,982 (GRCm39)	S241T	possibly damaging	Het
Or1j10	A	G	2: 36,267,355 (GRCm39)	D189G	possibly damaging	Het
Or4k77	A	T	2: 111,199,126 (GRCm39)	I50F	probably benign	Het
Or4x11	G	T	2: 89,868,138 (GRCm39)	V292L	probably benign	Het
Phldb2	A	G	16: 45,621,953 (GRCm39)	S676P	probably damaging	Het
Rttn	G	A	18: 89,066,541 (GRCm39)	E1196K	possibly damaging	Het
Slc13a3	G	A	2: 165,248,635 (GRCm39)	P548S	unknown	Het
Slc2a7	A	G	4: 150,244,467 (GRCm39)		probably benign	Het
Slc37a1	T	C	17: 31,547,135 (GRCm39)	S261P	possibly damaging	Het
Spryd3	T	A	15: 102,041,896 (GRCm39)	Y42F	possibly damaging	Het
Srrm3	A	G	5: 135,883,287 (GRCm39)		probably null	Het
Stambp	G	A	6: 83,533,372 (GRCm39)	T297I	probably damaging	Het
Sypl1	T	A	12: 33,017,668 (GRCm39)	Y129N	probably damaging	Het
Syt14	G	A	1: 192,662,843 (GRCm39)	P368S	possibly damaging	Het
Tas2r122	T	C	6: 132,688,227 (GRCm39)	D222G	probably damaging	Het
Tead2	C	A	7: 44,881,720 (GRCm39)	Y79*	probably null	Het
Uso1	T	C	5: 92,321,794 (GRCm39)	V229A	probably damaging	Het
Vmn1r238	A	G	18: 3,123,124 (GRCm39)	S97P	probably damaging	Het
Vmn2r82	T	A	10: 79,213,678 (GRCm39)	V88D	probably benign	Het
Wdr90	T	A	17: 26,076,194 (GRCm39)	S500C	probably damaging	Het
Zfp958	G	A	8: 4,675,967 (GRCm39)		probably null	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
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

2015-04-16