Mutagenetix > Incidental Mutation

Incidental Mutation 'R6154:Vps26a'

489455

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

044301-MU

Accession Numbers

Essential gene?

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

Stock #

R6154 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

62291014-62322584 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 62304119 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Aspartic acid at position 117 (E117D)

Ref Sequence

ENSEMBL: ENSMUSP00000151888 (fasta)

Gene Model

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

AlphaFold

P40336

Predicted Effect

probably benign
Transcript: ENSMUST00000092473
AA Change: E199D

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000090130
Gene: ENSMUSG00000020078
AA Change: E199D

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: E167D

PolyPhen 2 Score 0.028 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000101087
Gene: ENSMUSG00000020078
AA Change: E167D

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000217868
AA Change: E117D

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

Predicted Effect

probably benign
Transcript: ENSMUST00000219574

Meta Mutation Damage Score

0.4142

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.1%
20x: 94.8%

Validation Efficiency

97% (70/72)

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: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acss3	T	G	10: 106,959,210 (GRCm39)	I79L	probably benign	Het
Adam6a	C	T	12: 113,509,292 (GRCm39)	T555I	probably benign	Het
Adap1	A	G	5: 139,293,531 (GRCm39)	V60A	possibly damaging	Het
Afg3l2	G	T	18: 67,554,329 (GRCm39)	L458M	probably damaging	Het
Angpt1	T	C	15: 42,387,051 (GRCm39)	E101G	probably damaging	Het
Asxl2	T	C	12: 3,546,593 (GRCm39)	V459A	possibly damaging	Het
Cabs1	C	T	5: 88,127,613 (GRCm39)	T88I	possibly damaging	Het
Camta2	G	A	11: 70,569,211 (GRCm39)	A578V	probably damaging	Het
Cdc16	A	G	8: 13,818,609 (GRCm39)	N316D	possibly damaging	Het
Chrm3	T	A	13: 9,928,476 (GRCm39)	M187L	possibly damaging	Het
Clcn4	T	C	7: 7,294,481 (GRCm39)	T367A	probably benign	Het
Clcn7	T	C	17: 25,376,928 (GRCm39)	S654P	probably damaging	Het
Col6a3	T	A	1: 90,701,387 (GRCm39)	T2510S	unknown	Het
Crisp4	T	C	1: 18,193,012 (GRCm39)	E192G	possibly damaging	Het
Dmbt1	T	A	7: 130,711,370 (GRCm39)		probably null	Het
Dnah5	T	G	15: 28,204,177 (GRCm39)	L18R	probably benign	Het
Dnah9	T	G	11: 65,746,164 (GRCm39)	D3983A	probably benign	Het
Dock5	C	A	14: 68,097,361 (GRCm39)	V71L	probably benign	Het
Dync1h1	T	C	12: 110,584,427 (GRCm39)	V610A	probably damaging	Het
Dynlrb2	A	G	8: 117,242,428 (GRCm39)	Y86C	probably benign	Het
Ep400	T	C	5: 110,903,799 (GRCm39)	I267V	probably damaging	Het
Gaa	A	G	11: 119,169,178 (GRCm39)	Y575C	probably damaging	Het
Gm8094	T	A	14: 42,934,020 (GRCm39)	D24V	probably benign	Het
Grina	T	C	15: 76,133,087 (GRCm39)	I244T	possibly damaging	Het
Haus6	A	G	4: 86,501,993 (GRCm39)	L626P	possibly damaging	Het
Hexd	A	T	11: 121,112,097 (GRCm39)	H439L	probably benign	Het
Ifna12	A	T	4: 88,521,531 (GRCm39)	C5*	probably null	Het
Igf2bp2	G	T	16: 21,894,843 (GRCm39)	S300*	probably null	Het
Ighv6-5	T	C	12: 114,380,362 (GRCm39)	R71G	probably benign	Het
Lrrc37	A	G	11: 103,504,969 (GRCm39)	V2333A	probably benign	Het
Lrrn4cl	T	C	19: 8,829,252 (GRCm39)	S77P	probably damaging	Het
Mast4	A	G	13: 102,923,929 (GRCm39)	L302P	probably damaging	Het
Mink1	T	C	11: 70,500,927 (GRCm39)	V831A	possibly damaging	Het
Mme	T	A	3: 63,207,674 (GRCm39)	I40N	probably damaging	Het
Myh2	A	G	11: 67,077,438 (GRCm39)	T858A	probably benign	Het
Ncbp3	T	A	11: 72,940,700 (GRCm39)	Y67N	probably damaging	Het
Nedd1	T	A	10: 92,534,104 (GRCm39)	I349F	possibly damaging	Het
Nek11	A	T	9: 105,200,368 (GRCm39)	*81K	probably null	Het
Nrip1	A	G	16: 76,090,718 (GRCm39)	Y280H	probably damaging	Het
Obsl1	T	C	1: 75,476,788 (GRCm39)	D722G	probably benign	Het
Or10ag55-ps1	T	G	2: 87,139,902 (GRCm39)	S256R	probably benign	Het
Or2m12	A	T	16: 19,105,181 (GRCm39)	I104K	probably damaging	Het
Or4c29	A	G	2: 88,740,734 (GRCm39)	M1T	probably null	Het
Or5i1	A	G	2: 87,613,100 (GRCm39)	D72G	possibly damaging	Het
Or6c7	C	T	10: 129,323,545 (GRCm39)	T222I	probably damaging	Het
Pcdhb6	A	G	18: 37,467,966 (GRCm39)	I296V	probably benign	Het
Pcnx2	G	T	8: 126,489,552 (GRCm39)	L1681M	probably damaging	Het
Pdlim5	T	C	3: 141,983,674 (GRCm39)	R360G	possibly damaging	Het
Peli2	C	T	14: 48,488,051 (GRCm39)	Q81*	probably null	Het
Pitpnb	C	T	5: 111,486,263 (GRCm39)	Q56*	probably null	Het
Ppp1r3a	A	G	6: 14,754,603 (GRCm39)	S215P	possibly damaging	Het
Prrt3	A	G	6: 113,471,989 (GRCm39)	Y728H	probably damaging	Het
Rsf1	A	AAGGCGACGG	7: 97,229,111 (GRCm39)		probably null	Het
Rsf1	GCG	GCGACGGCGACG	7: 97,229,114 (GRCm39)		probably benign	Het
Sbno1	T	C	5: 124,516,542 (GRCm39)	H1277R	possibly damaging	Het
Siglecg	C	A	7: 43,061,441 (GRCm39)	N481K	possibly damaging	Het
Sirt6	C	T	10: 81,462,339 (GRCm39)	G20D	probably damaging	Het
Sit1	C	A	4: 43,482,981 (GRCm39)	R89S	probably benign	Het
Slc7a12	A	G	3: 14,546,094 (GRCm39)	R80G	probably damaging	Het
Smok3c	T	A	5: 138,062,747 (GRCm39)	M78K	probably benign	Het
Stk10	T	A	11: 32,553,654 (GRCm39)		probably null	Het
Tada2b	A	G	5: 36,634,008 (GRCm39)	V190A	probably damaging	Het
Tnk1	C	T	11: 69,747,780 (GRCm39)	V41I	probably damaging	Het
Tpr	T	A	1: 150,299,567 (GRCm39)	V1146E	probably benign	Het
Trappc9	T	C	15: 72,929,930 (GRCm39)	D142G	probably benign	Het
Trpm3	T	C	19: 22,965,178 (GRCm39)	Y1558H	probably damaging	Het
Unc5c	C	A	3: 141,383,914 (GRCm39)	S97R	probably damaging	Het
Vmn1r172	T	C	7: 23,359,583 (GRCm39)	I156T	probably damaging	Het
Vmn2r51	A	T	7: 9,821,921 (GRCm39)	M588K	possibly damaging	Het
Zfp451	A	T	1: 33,842,627 (GRCm39)		probably benign	Het
Zfp534	C	A	4: 147,759,145 (GRCm39)	R508I	probably benign	Het
Zp3r	C	T	1: 130,526,642 (GRCm39)	C187Y	probably damaging	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
R1563:Vps26a	UTSW	10	62,300,459 (GRCm39)	missense	probably benign	0.18
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
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'- GCTCAGTGGCTGGTAAAGATG -3'
(R):5'- TTAAAGCACCTGAATGTGACACAG -3'

Sequencing Primer
(F):5'- TGGCTGGTAAAGATGAAAATTATGTC -3'
(R):5'- TGTGACACAGGAGGTTCACTC -3'

Posted On

2017-10-10