Mutagenetix > Incidental Mutation

Incidental Mutation 'R1563:Vps26a'

170764

Institutional Source

Beutler Lab

Gene Symbol

Vps26a

Ensembl Gene

ENSMUSG00000020078

Gene Name

VPS26 retromer complex component A

Synonyms

HB58, Vps26, H beta 58

MMRRC Submission

039602-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.349) question?

Stock #

R1563 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

62291014-62322584 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 62300459 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Leucine at position 236 (I236L)

Ref Sequence

ENSEMBL: ENSMUSP00000090130 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000092473] [ENSMUST00000105447] [ENSMUST00000217868] [ENSMUST00000219574]

AlphaFold

P40336

PDB Structure

Structure of mouse VPS26A bound to rat SNX27 PDZ domain [X-RAY DIFFRACTION]

Predicted Effect

probably benign
Transcript: ENSMUST00000092473
AA Change: I236L

PolyPhen 2 Score 0.181 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000090130
Gene: ENSMUSG00000020078
AA Change: I236L

Domain	Start	End	E-Value	Type
low complexity region	20	32	N/A	INTRINSIC
Pfam:Vps26	40	315	3.7e-137	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000105447
AA Change: I204L

PolyPhen 2 Score 0.061 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000101087
Gene: ENSMUSG00000020078
AA Change: I204L

Domain	Start	End	E-Value	Type
Pfam:Vps26	8	283	2.7e-137	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000217868

Predicted Effect

probably benign
Transcript: ENSMUST00000219574

Meta Mutation Damage Score

0.3091

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.2%
20x: 92.4%

Validation Efficiency

98% (82/84)

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. The encoded protein is a component of a large multimeric complex, termed the retromer complex, involved in retrograde transport of proteins from endosomes to the trans-Golgi network. The close structural similarity between the yeast and human proteins that make up this complex suggests a similarity in function. Expression studies in yeast and mammalian cells indicate that this protein interacts directly with VPS35, which serves as the core of the retromer complex. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for a null mutation induced by transgene insertion exhibit retarded growth of the embryonic ectoderm beginning at embryonic day 7.5 and often, defects of the amnion and chorion. Mutant embryos arrest about day 9.5. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930519G04Rik	T	C	5: 115,001,569 (GRCm39)	M22T	probably benign	Het
A930018M24Rik	A	G	14: 51,134,576 (GRCm39)	L22P	probably damaging	Het
Aipl1	A	T	11: 71,927,538 (GRCm39)	M59K	probably damaging	Het
Atg2b	T	C	12: 105,589,747 (GRCm39)	I1835V	probably damaging	Het
Cacna1i	A	T	15: 80,274,056 (GRCm39)		probably benign	Het
Cacna1i	T	C	15: 80,205,389 (GRCm39)	V115A	probably damaging	Het
Catsperb	T	A	12: 101,554,361 (GRCm39)	M685K	probably damaging	Het
Cdh10	T	A	15: 18,986,853 (GRCm39)	Y361*	probably null	Het
Clcn4	C	T	7: 7,296,981 (GRCm39)	C219Y	probably damaging	Het
Cpeb2	G	A	5: 43,443,080 (GRCm39)	V924M	probably damaging	Het
Cpxm2	T	C	7: 131,745,411 (GRCm39)	E138G	probably benign	Het
Dennd1a	T	C	2: 37,748,441 (GRCm39)	Y346C	probably damaging	Het
Dnah8	T	A	17: 30,854,638 (GRCm39)	L100Q	probably benign	Het
Dnajc6	A	C	4: 101,456,334 (GRCm39)	N76T	probably damaging	Het
Ehbp1	A	G	11: 22,009,231 (GRCm39)	L954P	probably damaging	Het
Eral1	A	T	11: 77,966,232 (GRCm39)	D315E	probably benign	Het
Fbln2	G	T	6: 91,240,365 (GRCm39)	E724*	probably null	Het
Fyco1	A	G	9: 123,656,247 (GRCm39)		probably benign	Het
Fzd3	T	A	14: 65,473,173 (GRCm39)	E198D	probably damaging	Het
Fzd9	T	C	5: 135,279,408 (GRCm39)	N159S	probably damaging	Het
Galnt6	T	A	15: 100,601,259 (GRCm39)	Q340L	probably benign	Het
Gm20939	C	T	17: 95,184,522 (GRCm39)	A390V	probably damaging	Het
Gm5435	T	G	12: 82,542,464 (GRCm39)		noncoding transcript	Het
Gm9949	A	C	18: 62,317,089 (GRCm39)		probably benign	Het
Gprc5b	G	A	7: 118,582,984 (GRCm39)	T295I	probably benign	Het
Gria2	G	T	3: 80,598,704 (GRCm39)	Q777K	probably damaging	Het
Gtf3c3	C	T	1: 54,456,937 (GRCm39)	A488T	probably damaging	Het
Haao	T	C	17: 84,142,318 (GRCm39)	T174A	probably benign	Het
Hes6	A	T	1: 91,340,858 (GRCm39)	M1K	probably null	Het
Hook3	G	T	8: 26,600,780 (GRCm39)	Q43K	probably benign	Het
Klhl35	T	C	7: 99,120,902 (GRCm39)	V390A	probably damaging	Het
Myh9	G	T	15: 77,656,057 (GRCm39)	T1151K	probably damaging	Het
Nbn	A	T	4: 15,981,668 (GRCm39)	I587F	possibly damaging	Het
Nek4	A	G	14: 30,704,408 (GRCm39)	D696G	probably damaging	Het
Niban1	A	T	1: 151,591,424 (GRCm39)	Y522F	possibly damaging	Het
Nlrp2	T	C	7: 5,311,724 (GRCm39)	D52G	probably damaging	Het
Oit3	G	T	10: 59,263,896 (GRCm39)	R413S	probably damaging	Het
Or4k48	T	A	2: 111,476,027 (GRCm39)	H105L	probably damaging	Het
Or6c1b	A	G	10: 129,273,580 (GRCm39)	M300V	probably benign	Het
Otof	T	C	5: 30,528,349 (GRCm39)	T1870A	probably benign	Het
Pdgfd	T	C	9: 6,293,939 (GRCm39)		probably null	Het
Pitrm1	T	C	13: 6,613,506 (GRCm39)	V526A	possibly damaging	Het
Pknox1	T	C	17: 31,814,256 (GRCm39)	S194P	probably damaging	Het
Plekhg5	T	C	4: 152,181,266 (GRCm39)	S8P	probably benign	Het
Ppp1r13b	T	C	12: 111,807,416 (GRCm39)	E157G	probably damaging	Het
Psmd3	C	T	11: 98,585,051 (GRCm39)	R466W	probably damaging	Het
Ptgfrn	A	G	3: 100,967,967 (GRCm39)	F542S	possibly damaging	Het
Ptgs1	A	T	2: 36,135,214 (GRCm39)	M393L	possibly damaging	Het
Qpct	T	A	17: 79,371,492 (GRCm39)	S87T	probably benign	Het
Qtrt1	T	A	9: 21,330,607 (GRCm39)	V269D	probably benign	Het
Rassf9	C	G	10: 102,380,821 (GRCm39)	R68G	probably damaging	Het
Relch	A	G	1: 105,647,259 (GRCm39)	Y707C	probably damaging	Het
Rif1	A	G	2: 51,963,235 (GRCm39)	E25G	probably damaging	Het
Rnf213	T	C	11: 119,305,352 (GRCm39)	F528L	probably benign	Het
Sgip1	T	C	4: 102,823,457 (GRCm39)	S693P	probably benign	Het
She	A	G	3: 89,761,921 (GRCm39)	D460G	probably benign	Het
Sipa1l1	G	T	12: 82,387,935 (GRCm39)	V54L	probably benign	Het
Slc8a3	T	A	12: 81,251,781 (GRCm39)	D640V	possibly damaging	Het
Smurf1	T	A	5: 144,819,323 (GRCm39)	E601D	probably damaging	Het
Sned1	G	A	1: 93,209,376 (GRCm39)	V830M	possibly damaging	Het
Synpo2l	A	G	14: 20,711,346 (GRCm39)	S425P	probably damaging	Het
Tbck	T	C	3: 132,421,454 (GRCm39)	V187A	possibly damaging	Het
Tcf23	A	T	5: 31,126,175 (GRCm39)	H18L	probably benign	Het
Tcp11l2	A	G	10: 84,420,808 (GRCm39)	S16G	probably damaging	Het
Tekt2	T	A	4: 126,217,200 (GRCm39)	M233L	probably benign	Het
Tex14	T	C	11: 87,427,634 (GRCm39)	S29P	probably damaging	Het
Tjp2	T	A	19: 24,110,067 (GRCm39)	N59I	probably damaging	Het
Tlr5	G	A	1: 182,802,575 (GRCm39)	M626I	probably benign	Het
Tnn	A	T	1: 159,952,985 (GRCm39)	V685D	probably damaging	Het
Trappc9	G	A	15: 72,897,816 (GRCm39)	R377W	probably damaging	Het
Trhr	G	A	15: 44,060,497 (GRCm39)	V6I	probably benign	Het
Trim30c	C	T	7: 104,032,158 (GRCm39)	R301Q	probably benign	Het
Usp51	T	C	X: 151,790,988 (GRCm39)	I194T	probably benign	Het
Vmn2r63	A	G	7: 42,553,550 (GRCm39)	S569P	probably benign	Het
Zc3h7b	C	T	15: 81,661,289 (GRCm39)	P376L	probably benign	Het
Zcchc14	T	C	8: 122,330,718 (GRCm39)	M882V	probably benign	Het
Zfhx2	A	G	14: 55,302,545 (GRCm39)	V1813A	probably benign	Het
Zswim2	C	T	2: 83,745,626 (GRCm39)	G604D	possibly damaging	Het
Zzef1	C	T	11: 72,739,559 (GRCm39)	Q669*	probably null	Het

Other mutations in Vps26a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R0566:Vps26a	UTSW	10	62,316,325 (GRCm39)	splice site	probably benign
R0801:Vps26a	UTSW	10	62,294,857 (GRCm39)	splice site	probably benign
R0856:Vps26a	UTSW	10	62,304,189 (GRCm39)	missense	possibly damaging	0.84
R1785:Vps26a	UTSW	10	62,304,176 (GRCm39)	missense	probably benign	0.01
R1833:Vps26a	UTSW	10	62,294,825 (GRCm39)	missense	probably benign	0.00
R2173:Vps26a	UTSW	10	62,304,171 (GRCm39)	missense	probably damaging	1.00
R4516:Vps26a	UTSW	10	62,304,124 (GRCm39)	missense	probably damaging	1.00
R5339:Vps26a	UTSW	10	62,294,746 (GRCm39)	missense	probably damaging	1.00
R5391:Vps26a	UTSW	10	62,292,526 (GRCm39)	makesense	probably null
R5646:Vps26a	UTSW	10	62,304,077 (GRCm39)	missense	probably damaging	1.00
R6154:Vps26a	UTSW	10	62,304,119 (GRCm39)	missense	probably damaging	1.00
R8995:Vps26a	UTSW	10	62,300,458 (GRCm39)	missense	probably damaging	1.00
R9468:Vps26a	UTSW	10	62,300,516 (GRCm39)	missense	probably damaging	1.00
R9645:Vps26a	UTSW	10	62,305,791 (GRCm39)	missense	probably benign	0.12
R9762:Vps26a	UTSW	10	62,316,433 (GRCm39)	missense	probably benign	0.17

Predicted Primers

PCR Primer
(F):5'- GCCTTCAGGGGCATGGAAGTCTATT -3'
(R):5'- AGATAATTGCgggctggcaagatg -3'

Sequencing Primer
(F):5'- GCATGGAAGTCTATTCAGCTCAAG -3'
(R):5'- GTGACACATACTCTTTCCAAATAGGT -3'

Posted On

2014-04-13