Mutagenetix > Incidental Mutation

Incidental Mutation 'R2055:Vps41'

226616

Institutional Source

Beutler Lab

Gene Symbol

Vps41

Ensembl Gene

ENSMUSG00000041236

Gene Name

VPS41 HOPS complex subunit

Synonyms

Vam2, mVam2

MMRRC Submission

040060-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2055 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

18901462-19050981 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 19038786 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 737 (N737K)

Ref Sequence

ENSEMBL: ENSMUSP00000072729 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000072961]

AlphaFold

Q5KU39

Predicted Effect

possibly damaging
Transcript: ENSMUST00000072961
AA Change: N737K

PolyPhen 2 Score 0.948 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000072729
Gene: ENSMUSG00000041236
AA Change: N737K

Domain	Start	End	E-Value	Type
low complexity region	3	26	N/A	INTRINSIC
Blast:WD40	34	70	2e-7	BLAST
SCOP:d1flga_	44	253	6e-9	SMART
Blast:WD40	159	195	3e-11	BLAST
CLH	570	711	1.92e-42	SMART
RING	790	837	8.98e-2	SMART

Meta Mutation Damage Score

0.0912

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.3%

Validation Efficiency

100% (74/74)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene encodes the human ortholog of yeast Vps41 protein which is also conserved in Drosophila, tomato, and Arabidopsis. Expression studies in yeast and human indicate that this protein may be involved in the formation and fusion of transport vesicles from the Golgi. Several transcript variants encoding different isoforms have been described for this gene, however, the full-length nature of not all is known. [provided by RefSeq, Jul 2008]
PHENOTYPE: Embryos homozygous for a knock-out allele die by E9 exhibiting morphological and functional alteration of late endocytic compartments, and abnormal triploblastic development. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700123K08Rik	T	C	5: 138,561,107 (GRCm39)	E185G	probably damaging	Het
3425401B19Rik	A	G	14: 32,384,508 (GRCm39)	S486P	probably benign	Het
A630023A22Rik	T	C	14: 33,774,707 (GRCm39)		probably benign	Het
Abca1	T	C	4: 53,069,881 (GRCm39)	N1271S	probably benign	Het
AI597479	C	T	1: 43,150,280 (GRCm39)	A130V	probably benign	Het
Angptl4	A	G	17: 33,999,498 (GRCm39)		probably null	Het
Arhgef25	T	A	10: 127,021,004 (GRCm39)	N294I	probably damaging	Het
Atp2b1	T	C	10: 98,850,421 (GRCm39)	V848A	probably damaging	Het
Bard1	T	C	1: 71,114,031 (GRCm39)	T317A	probably benign	Het
C1rl	T	C	6: 124,470,781 (GRCm39)	W30R	probably benign	Het
Cchcr1	A	G	17: 35,837,317 (GRCm39)	E379G	probably damaging	Het
Cfap36	G	T	11: 29,197,122 (GRCm39)	A3E	probably damaging	Het
Cilp	G	A	9: 65,186,997 (GRCm39)	G1031S	probably damaging	Het
Clca4a	A	G	3: 144,676,489 (GRCm39)	Y64H	probably damaging	Het
Cops5	A	G	1: 10,102,562 (GRCm39)		probably null	Het
Cracr2a	G	T	6: 127,585,564 (GRCm39)	E121*	probably null	Het
Cstf1	A	G	2: 172,222,403 (GRCm39)	E387G	probably benign	Het
D630044L22Rik	A	C	17: 26,180,951 (GRCm39)	D733E	probably damaging	Het
Dlc1	A	T	8: 37,060,535 (GRCm39)	C514S	probably damaging	Het
Dmwd	G	T	7: 18,810,610 (GRCm39)	R139L	probably benign	Het
Dnah17	A	T	11: 117,958,357 (GRCm39)	S2709T	probably benign	Het
Dnmt3a	T	C	12: 3,922,859 (GRCm39)	I154T	probably benign	Het
Dpp7	T	C	2: 25,244,490 (GRCm39)	N297S	possibly damaging	Het
Ern2	A	T	7: 121,783,168 (GRCm39)	V34D	possibly damaging	Het
Erp27	A	G	6: 136,885,227 (GRCm39)		probably benign	Het
F2	T	C	2: 91,458,787 (GRCm39)	T508A	probably benign	Het
Fam181b	A	G	7: 92,729,634 (GRCm39)	T136A	probably benign	Het
Fam227b	C	A	2: 125,942,874 (GRCm39)	V308L	probably benign	Het
Fbxw20	A	T	9: 109,050,442 (GRCm39)	H394Q	probably damaging	Het
G530012D18Rik	CAGAGAGA	CAGAGAGAGA	1: 85,504,945 (GRCm39)		probably null	Het
Glt8d1	T	G	14: 30,731,693 (GRCm39)	S111A	probably benign	Het
Gm11146	A	T	16: 77,391,969 (GRCm39)		probably benign	Het
Grip1	C	T	10: 119,885,416 (GRCm39)		probably benign	Het
H2-Q2	A	T	17: 35,564,247 (GRCm39)	T334S	probably benign	Het
Hcrtr1	A	G	4: 130,024,680 (GRCm39)	V402A	probably benign	Het
Hmcn2	C	A	2: 31,268,294 (GRCm39)	A1130D	probably benign	Het
Hsd17b2	T	C	8: 118,428,913 (GRCm39)	L60P	possibly damaging	Het
Htr1f	A	T	16: 64,746,398 (GRCm39)	I298N	probably damaging	Het
Ighmbp2	G	T	19: 3,315,095 (GRCm39)	A775D	probably benign	Het
Kcnn3	A	G	3: 89,428,682 (GRCm39)	T303A	probably damaging	Het
Kiz	C	A	2: 146,733,203 (GRCm39)	Q460K	probably benign	Het
Krt75	C	T	15: 101,481,196 (GRCm39)	V193I	probably benign	Het
Lsp1	G	A	7: 142,043,144 (GRCm39)		probably null	Het
Mfsd12	A	G	10: 81,196,063 (GRCm39)	H146R	probably damaging	Het
Mmp23	T	C	4: 155,736,444 (GRCm39)	K199R	possibly damaging	Het
Naip2	A	G	13: 100,315,880 (GRCm39)	V300A	probably benign	Het
Nbeal1	C	T	1: 60,350,216 (GRCm39)	L2422F	probably damaging	Het
Nbeal2	G	T	9: 110,464,375 (GRCm39)	D1094E	possibly damaging	Het
Nckap5	T	C	1: 125,954,635 (GRCm39)	E639G	probably damaging	Het
Nr4a3	A	G	4: 48,067,771 (GRCm39)	I456V	possibly damaging	Het
Or2t43	A	G	11: 58,457,673 (GRCm39)	F166S	probably damaging	Het
Parp9	G	T	16: 35,773,984 (GRCm39)	V86L	probably damaging	Het
Phactr1	A	G	13: 43,231,416 (GRCm39)	N386S	probably damaging	Het
Pold2	A	T	11: 5,823,516 (GRCm39)	Y304*	probably null	Het
Pou5f2	A	G	13: 78,173,940 (GRCm39)	Y294C	probably benign	Het
Rars1	A	G	11: 35,717,410 (GRCm39)		probably benign	Het
Rbm12b1	A	G	4: 12,145,606 (GRCm39)	E526G	probably benign	Het
Sacs	T	C	14: 61,451,498 (GRCm39)	Y4515H	probably damaging	Het
Sdk2	C	A	11: 113,741,780 (GRCm39)	R813L	probably damaging	Het
Six5	T	C	7: 18,829,154 (GRCm39)	V198A	possibly damaging	Het
Slco1a7	A	T	6: 141,671,181 (GRCm39)	H430Q	probably benign	Het
Spata31e2	A	T	1: 26,724,813 (GRCm39)	N122K	possibly damaging	Het
Spn	A	G	7: 126,736,388 (GRCm39)	S40P	probably damaging	Het
Ssr1	A	G	13: 38,171,761 (GRCm39)		probably benign	Het
Tlr6	C	A	5: 65,111,269 (GRCm39)	C546F	probably damaging	Het
Top1	T	A	2: 160,544,748 (GRCm39)		probably benign	Het
Trhr2	A	G	8: 123,085,532 (GRCm39)	S151P	probably damaging	Het
Tubb2b	T	G	13: 34,311,708 (GRCm39)	K362Q	probably benign	Het
Unc13c	T	C	9: 73,643,832 (GRCm39)	T1211A	probably damaging	Het
Vmn1r15	T	C	6: 57,235,729 (GRCm39)	V199A	possibly damaging	Het
Vnn1	A	G	10: 23,776,475 (GRCm39)		probably benign	Het
Vps50	T	A	6: 3,522,265 (GRCm39)	N144K	probably benign	Het
Zc3h7a	A	T	16: 10,955,340 (GRCm39)	N911K	probably benign	Het
Zkscan7	T	A	9: 122,718,002 (GRCm39)	S132R	probably damaging	Het

Other mutations in Vps41

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01134:Vps41	APN	13	19,050,320 (GRCm39)	missense	probably benign	0.37
IGL01563:Vps41	APN	13	18,966,897 (GRCm39)	splice site	probably benign
IGL01880:Vps41	APN	13	18,994,641 (GRCm39)	missense	probably benign	0.01
IGL02024:Vps41	APN	13	18,975,827 (GRCm39)	splice site	probably benign
IGL02458:Vps41	APN	13	19,037,649 (GRCm39)	missense	possibly damaging	0.67
IGL02740:Vps41	APN	13	19,022,850 (GRCm39)	missense	probably damaging	1.00
IGL03218:Vps41	APN	13	19,013,440 (GRCm39)	missense	possibly damaging	0.74
R0197:Vps41	UTSW	13	19,038,833 (GRCm39)	critical splice donor site	probably null
R0284:Vps41	UTSW	13	19,037,610 (GRCm39)	missense	probably damaging	1.00
R0321:Vps41	UTSW	13	19,026,465 (GRCm39)	splice site	probably benign
R0372:Vps41	UTSW	13	19,026,417 (GRCm39)	missense	probably benign	0.00
R0382:Vps41	UTSW	13	19,011,897 (GRCm39)	missense	probably benign	0.30
R1691:Vps41	UTSW	13	19,025,413 (GRCm39)	missense	probably damaging	1.00
R2082:Vps41	UTSW	13	19,036,521 (GRCm39)	missense	probably benign	0.27
R2147:Vps41	UTSW	13	19,023,904 (GRCm39)	splice site	probably null
R2897:Vps41	UTSW	13	18,994,598 (GRCm39)	splice site	probably benign
R4322:Vps41	UTSW	13	19,007,960 (GRCm39)	missense	probably damaging	1.00
R4600:Vps41	UTSW	13	18,929,453 (GRCm39)	missense	probably damaging	0.97
R4751:Vps41	UTSW	13	18,995,792 (GRCm39)	missense	probably damaging	0.98
R4856:Vps41	UTSW	13	19,013,425 (GRCm39)	missense	probably damaging	0.98
R5389:Vps41	UTSW	13	19,046,708 (GRCm39)	missense	probably damaging	0.99
R7022:Vps41	UTSW	13	19,026,438 (GRCm39)	missense	possibly damaging	0.76
R7456:Vps41	UTSW	13	19,048,204 (GRCm39)	missense	probably benign	0.02
R7747:Vps41	UTSW	13	19,025,422 (GRCm39)	critical splice donor site	probably null
R7790:Vps41	UTSW	13	19,026,438 (GRCm39)	missense	possibly damaging	0.76
R8029:Vps41	UTSW	13	19,007,955 (GRCm39)	nonsense	probably null
R8033:Vps41	UTSW	13	18,994,635 (GRCm39)	missense	possibly damaging	0.94
R8241:Vps41	UTSW	13	19,033,168 (GRCm39)	missense	possibly damaging	0.73
R8267:Vps41	UTSW	13	18,994,641 (GRCm39)	missense	probably benign	0.00
R8801:Vps41	UTSW	13	18,998,403 (GRCm39)	missense	possibly damaging	0.78
R8927:Vps41	UTSW	13	18,929,501 (GRCm39)	missense	probably benign	0.01
R8928:Vps41	UTSW	13	18,929,501 (GRCm39)	missense	probably benign	0.01
R9029:Vps41	UTSW	13	18,994,723 (GRCm39)	critical splice donor site	probably null
R9057:Vps41	UTSW	13	19,027,702 (GRCm39)	missense	probably benign	0.19
R9066:Vps41	UTSW	13	19,008,018 (GRCm39)	missense	probably damaging	0.99
R9113:Vps41	UTSW	13	19,023,883 (GRCm39)	missense	probably benign	0.25
R9129:Vps41	UTSW	13	19,011,775 (GRCm39)	missense	probably benign	0.00
R9282:Vps41	UTSW	13	19,013,401 (GRCm39)	nonsense	probably null
R9391:Vps41	UTSW	13	18,994,616 (GRCm39)	missense	probably benign	0.19
R9478:Vps41	UTSW	13	19,046,913 (GRCm39)	missense
R9569:Vps41	UTSW	13	19,013,396 (GRCm39)	missense	possibly damaging	0.93
Z1177:Vps41	UTSW	13	19,038,765 (GRCm39)	missense	probably damaging	0.97
Z1177:Vps41	UTSW	13	19,030,105 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- AGATGGTCTCAGTTTCTCCTTTTAG -3'
(R):5'- TGCAAAGTGTAACAGGCATCC -3'

Sequencing Primer
(F):5'- ACTTAAAGAGGATTGGTTCTTGAGAG -3'
(R):5'- CCAAATGGCCTGCAAATACTTATG -3'

Posted On

2014-09-17