Mutagenetix > Incidental Mutation

Incidental Mutation 'R0565:Vps25'

46140

Institutional Source

Beutler Lab

Gene Symbol

Vps25

Ensembl Gene

ENSMUSG00000078656

Gene Name

vacuolar protein sorting 25

Synonyms

D11Wsu68e, 1110020N13Rik

MMRRC Submission

038756-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0565 (G1)

Quality Score

150

Status

Validated

Chromosome

Chromosomal Location

101144533-101150375 bp(+) (GRCm39)

Type of Mutation

unclassified

DNA Base Change (assembly)

T to C at 101149731 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000131298 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000007533] [ENSMUST00000042477] [ENSMUST00000100414] [ENSMUST00000103108] [ENSMUST00000107280] [ENSMUST00000121331] [ENSMUST00000144306] [ENSMUST00000128260] [ENSMUST00000139487] [ENSMUST00000147741]

AlphaFold

Q9CQ80

Predicted Effect

probably benign
Transcript: ENSMUST00000007533

SMART Domains

Protein: ENSMUSP00000007533
Gene: ENSMUSG00000078656

Domain	Start	End	E-Value	Type
Pfam:ESCRT-II	10	147	1e-55	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000042477

SMART Domains

Protein: ENSMUSP00000042088
Gene: ENSMUSG00000078656

Domain	Start	End	E-Value	Type
Pfam:ESCRT-II	9	147	1.3e-64	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000100414

SMART Domains

Protein: ENSMUSP00000097981
Gene: ENSMUSG00000078656

Domain	Start	End	E-Value	Type
Pfam:ESCRT-II	9	144	5e-61	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000103108

SMART Domains

Protein: ENSMUSP00000099397
Gene: ENSMUSG00000035112

Domain	Start	End	E-Value	Type
low complexity region	31	45	N/A	INTRINSIC
low complexity region	52	64	N/A	INTRINSIC
low complexity region	76	92	N/A	INTRINSIC
low complexity region	95	105	N/A	INTRINSIC
low complexity region	126	155	N/A	INTRINSIC
Pfam:Pkinase_Tyr	171	427	4.7e-42	PFAM
Pfam:Pkinase	171	429	9e-55	PFAM
Pfam:OSR1_C	450	486	3e-18	PFAM
low complexity region	503	513	N/A	INTRINSIC
low complexity region	516	530	N/A	INTRINSIC
low complexity region	544	560	N/A	INTRINSIC
low complexity region	627	638	N/A	INTRINSIC
low complexity region	660	678	N/A	INTRINSIC
low complexity region	757	778	N/A	INTRINSIC
low complexity region	793	808	N/A	INTRINSIC
low complexity region	841	877	N/A	INTRINSIC
low complexity region	882	915	N/A	INTRINSIC
low complexity region	921	951	N/A	INTRINSIC
low complexity region	1014	1033	N/A	INTRINSIC
low complexity region	1093	1112	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000107280

SMART Domains

Protein: ENSMUSP00000102901
Gene: ENSMUSG00000078656

Domain	Start	End	E-Value	Type
Pfam:ESCRT-II	10	153	7.2e-56	PFAM
low complexity region	155	166	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000121331

SMART Domains

Protein: ENSMUSP00000114100
Gene: ENSMUSG00000078656

Domain	Start	End	E-Value	Type
Pfam:ESCRT-II	1	99	1.8e-41	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000123529

Predicted Effect

probably benign
Transcript: ENSMUST00000144306

SMART Domains

Protein: ENSMUSP00000131026
Gene: ENSMUSG00000078656

Domain	Start	End	E-Value	Type
Pfam:ESCRT-II	9	91	2.5e-34	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000128260

SMART Domains

Protein: ENSMUSP00000127718
Gene: ENSMUSG00000001240

Domain	Start	End	E-Value	Type
signal peptide	1	44	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000139487

SMART Domains

Protein: ENSMUSP00000129666
Gene: ENSMUSG00000035112

Domain	Start	End	E-Value	Type
low complexity region	31	45	N/A	INTRINSIC
low complexity region	52	64	N/A	INTRINSIC
low complexity region	76	92	N/A	INTRINSIC
low complexity region	95	105	N/A	INTRINSIC
low complexity region	126	155	N/A	INTRINSIC
Pfam:Pkinase_Tyr	171	242	4e-8	PFAM
Pfam:Pkinase	171	252	1.9e-10	PFAM
low complexity region	269	283	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000147741

SMART Domains

Protein: ENSMUSP00000131298
Gene: ENSMUSG00000035112

Domain	Start	End	E-Value	Type
low complexity region	31	45	N/A	INTRINSIC
low complexity region	52	64	N/A	INTRINSIC
low complexity region	76	92	N/A	INTRINSIC
low complexity region	95	105	N/A	INTRINSIC
low complexity region	126	155	N/A	INTRINSIC
Pfam:Pkinase	171	394	9.3e-50	PFAM
Pfam:Pkinase_Tyr	171	399	3.7e-38	PFAM
low complexity region	401	413	N/A	INTRINSIC

Coding Region Coverage

1x: 99.6%
3x: 98.8%
10x: 96.8%
20x: 93.6%

Validation Efficiency

100% (73/73)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that is a subunit of the endosomal sorting complex required for transport II (ESCRT-II). This protein complex functions in sorting of ubiquitinated membrane proteins during endocytosis. A pseudogene of this gene is present on chromosome 1. [provided by RefSeq, Jul 2013]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit embryonic lethality before E8.5. Mice homozygous for a hypomorphic allele exhibit short limbs, polydactyly and craniofacial defects. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930562C15Rik	A	T	16: 4,682,200 (GRCm39)	H1010L	probably benign	Het
A2ml1	C	A	6: 128,545,706 (GRCm39)	E474*	probably null	Het
Agtr1b	T	C	3: 20,369,838 (GRCm39)	H256R	probably damaging	Het
Amacr	C	T	15: 10,982,032 (GRCm39)	A46V	possibly damaging	Het
Atosb	A	T	4: 43,034,647 (GRCm39)		probably benign	Het
Cabp5	A	T	7: 13,135,260 (GRCm39)	M67L	probably damaging	Het
Caskin2	T	C	11: 115,691,842 (GRCm39)	E981G	probably damaging	Het
Ccdc88a	A	G	11: 29,411,042 (GRCm39)		probably benign	Het
Cd180	A	G	13: 102,839,382 (GRCm39)		probably benign	Het
Cd200l1	T	A	16: 45,264,536 (GRCm39)		probably benign	Het
Cemip	G	A	7: 83,613,318 (GRCm39)	H627Y	probably damaging	Het
Cep131	G	T	11: 119,964,588 (GRCm39)	H289Q	probably damaging	Het
Cep350	G	A	1: 155,836,941 (GRCm39)		probably benign	Het
Cfap52	A	T	11: 67,840,425 (GRCm39)	C169S	probably benign	Het
Cps1	A	T	1: 67,205,608 (GRCm39)	T544S	possibly damaging	Het
Cul7	T	C	17: 46,962,929 (GRCm39)	S187P	probably damaging	Het
Dhx40	C	A	11: 86,661,993 (GRCm39)	R688L	probably damaging	Het
E330034G19Rik	C	A	14: 24,356,985 (GRCm39)	Q174K	probably benign	Het
Efna5	T	C	17: 63,188,031 (GRCm39)	Y32C	probably damaging	Het
Ethe1	A	G	7: 24,307,314 (GRCm39)	H176R	probably benign	Het
Exoc3	A	G	13: 74,330,394 (GRCm39)		probably null	Het
Fam135b	T	A	15: 71,362,686 (GRCm39)	N232Y	possibly damaging	Het
Fndc9	C	T	11: 46,128,984 (GRCm39)	L168F	probably damaging	Het
Fpr-rs3	G	A	17: 20,844,283 (GRCm39)	A286V	probably damaging	Het
Immt	T	A	6: 71,823,467 (GRCm39)		probably benign	Het
Ipo7	T	C	7: 109,648,800 (GRCm39)		probably benign	Het
Ipo8	A	T	6: 148,688,221 (GRCm39)	L747H	probably damaging	Het
Ireb2	A	T	9: 54,807,267 (GRCm39)	N610Y	probably damaging	Het
Irs2	A	G	8: 11,054,592 (GRCm39)	V1280A	probably damaging	Het
Kcnj3	T	A	2: 55,485,276 (GRCm39)	M458K	probably benign	Het
Kl	A	G	5: 150,904,409 (GRCm39)	K387R	possibly damaging	Het
L3mbtl2	C	A	15: 81,568,487 (GRCm39)		probably benign	Het
Lamb1	A	C	12: 31,348,914 (GRCm39)	I649L	probably benign	Het
Lipm	A	C	19: 34,093,906 (GRCm39)	L274F	probably benign	Het
Lrfn3	A	G	7: 30,060,216 (GRCm39)	V3A	probably benign	Het
Lrrc8c	A	C	5: 105,754,894 (GRCm39)	D223A	probably damaging	Het
Ltn1	C	A	16: 87,212,898 (GRCm39)	K554N	probably benign	Het
Mertk	T	C	2: 128,613,403 (GRCm39)	I473T	probably benign	Het
Mfsd12	C	A	10: 81,197,243 (GRCm39)	N245K	probably benign	Het
Mmp16	A	G	4: 17,987,705 (GRCm39)	D89G	probably damaging	Het
Myo5a	T	A	9: 75,087,394 (GRCm39)	N1083K	probably benign	Het
Ncapd3	C	T	9: 26,999,294 (GRCm39)	A1290V	probably benign	Het
Nefm	A	G	14: 68,362,070 (GRCm39)	S65P	probably damaging	Het
Nt5c2	C	T	19: 46,886,064 (GRCm39)	R220H	probably damaging	Het
Or4c102	T	A	2: 88,422,353 (GRCm39)	D68E	probably benign	Het
Osbpl1a	A	T	18: 12,892,501 (GRCm39)	S438R	probably damaging	Het
Pcdhb5	T	C	18: 37,453,820 (GRCm39)	S67P	possibly damaging	Het
Per3	A	T	4: 151,118,409 (GRCm39)	I228N	probably damaging	Het
Pnpla7	T	G	2: 24,870,129 (GRCm39)		probably benign	Het
Ppp1r15b	G	T	1: 133,064,391 (GRCm39)		probably benign	Het
Psmd2	G	T	16: 20,479,176 (GRCm39)	L678F	probably null	Het
Ptch2	A	G	4: 116,963,340 (GRCm39)		probably benign	Het
Ranbp2	T	A	10: 58,312,158 (GRCm39)	D959E	probably benign	Het
Rph3al	C	T	11: 75,724,227 (GRCm39)		probably null	Het
Sec31b	T	A	19: 44,512,992 (GRCm39)	E499V	probably damaging	Het
Sel1l	T	C	12: 91,778,663 (GRCm39)	I667M	probably benign	Het
Sel1l	C	A	12: 91,780,719 (GRCm39)	V641L	possibly damaging	Het
Slc7a1	T	A	5: 148,288,879 (GRCm39)	I123F	probably damaging	Het
Smarca2	G	A	19: 26,659,275 (GRCm39)	R855Q	possibly damaging	Het
Sphk1	G	T	11: 116,427,184 (GRCm39)		probably benign	Het
Spink12	C	A	18: 44,237,755 (GRCm39)	S11*	probably null	Het
Sstr2	A	T	11: 113,516,445 (GRCm39)	I342F	probably benign	Het
Stxbp1	T	C	2: 32,709,860 (GRCm39)	T78A	probably benign	Het
Trim11	T	A	11: 58,881,410 (GRCm39)	S434R	probably damaging	Het
Ubr2	T	C	17: 47,266,812 (GRCm39)	E1113G	probably damaging	Het
Upb1	T	A	10: 75,264,188 (GRCm39)		probably benign	Het
Vit	T	A	17: 78,932,266 (GRCm39)	C458S	probably damaging	Het
Vmn1r58	T	C	7: 5,414,165 (GRCm39)	I22V	probably benign	Het
Wbp2	G	T	11: 115,973,211 (GRCm39)	D65E	possibly damaging	Het
Wdr72	A	G	9: 74,124,588 (GRCm39)	D980G	probably benign	Het
Xkr8	A	C	4: 132,458,228 (GRCm39)		probably null	Het

Other mutations in Vps25

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01389:Vps25	APN	11	101,144,861 (GRCm39)	nonsense	probably null
IGL02795:Vps25	APN	11	101,146,916 (GRCm39)	missense	probably damaging	1.00
IGL03157:Vps25	APN	11	101,147,723 (GRCm39)	missense	probably benign	0.04
R4169:Vps25	UTSW	11	101,144,918 (GRCm39)	missense	probably damaging	0.96
R4773:Vps25	UTSW	11	101,149,655 (GRCm39)	missense	probably benign	0.35
R6586:Vps25	UTSW	11	101,149,835 (GRCm39)	missense	probably damaging	1.00
R7290:Vps25	UTSW	11	101,149,775 (GRCm39)	missense	probably damaging	1.00
R9342:Vps25	UTSW	11	101,149,623 (GRCm39)	missense	probably damaging	1.00
R9719:Vps25	UTSW	11	101,146,853 (GRCm39)	missense	probably null	1.00

Predicted Primers

PCR Primer
(F):5'- TTCTACTCCGTACTCCCCAGGAATG -3'
(R):5'- TCTGAGCTTTCAGGACTTGAGCCC -3'

Sequencing Primer
(F):5'- CCAGGAATGCCCAGGAATTG -3'
(R):5'- GAGTGACAGATCCAGTCTGTG -3'

Posted On

2013-06-11