Mutagenetix > Incidental Mutation

Incidental Mutation 'R4169:Vps25'

320705

Institutional Source

Beutler Lab

Gene Symbol

Vps25

Ensembl Gene

ENSMUSG00000078656

Gene Name

vacuolar protein sorting 25

Synonyms

D11Wsu68e, 1110020N13Rik

MMRRC Submission

041010-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4169 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

101144533-101150375 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 101144918 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 39 (S39P)

Ref Sequence

ENSEMBL: ENSMUSP00000042088 (fasta)

Gene Model

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

AlphaFold

Q9CQ80

Predicted Effect

probably damaging
Transcript: ENSMUST00000007533
AA Change: S39P

PolyPhen 2 Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000007533
Gene: ENSMUSG00000078656
AA Change: S39P

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000042477
AA Change: S39P

PolyPhen 2 Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000042088
Gene: ENSMUSG00000078656
AA Change: S39P

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000100414
AA Change: S39P

PolyPhen 2 Score 0.793 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000097981
Gene: ENSMUSG00000078656
AA Change: S39P

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000107280
AA Change: S39P

PolyPhen 2 Score 0.605 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000102901
Gene: ENSMUSG00000078656
AA Change: S39P

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: ENSMUST00000128260

SMART Domains

Protein: ENSMUSP00000127718
Gene: ENSMUSG00000001240

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000144306
AA Change: S39P

PolyPhen 2 Score 0.805 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000131026
Gene: ENSMUSG00000078656
AA Change: S39P

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

Meta Mutation Damage Score

0.3780

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.8%

Validation Efficiency

98% (48/49)

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: 43 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acot7	T	C	4: 152,302,250 (GRCm39)	C121R	probably damaging	Het
Ampd1	T	A	3: 103,002,157 (GRCm39)	M546K	probably damaging	Het
Birc2	T	A	9: 7,849,684 (GRCm39)	D535V	possibly damaging	Het
Btn1a1	A	G	13: 23,649,325 (GRCm39)	L9P	probably benign	Het
Cmip	A	T	8: 118,183,656 (GRCm39)	N743I	probably damaging	Het
Col4a2	C	T	8: 11,479,391 (GRCm39)	P758L	probably benign	Het
Ddx50	A	T	10: 62,476,549 (GRCm39)	Y241*	probably null	Het
Elk3	A	G	10: 93,101,197 (GRCm39)		probably null	Het
Fbn1	T	C	2: 125,205,872 (GRCm39)	T1042A	possibly damaging	Het
Gm5445	A	G	13: 12,393,527 (GRCm39)		noncoding transcript	Het
Gnat3	T	C	5: 18,208,862 (GRCm39)	F189L	probably damaging	Het
Hectd1	T	C	12: 51,837,008 (GRCm39)	T815A	probably damaging	Het
Hmcn1	A	C	1: 150,471,750 (GRCm39)		probably null	Het
Hrc	A	G	7: 44,986,181 (GRCm39)	D444G	probably benign	Het
Ighv1-53	T	A	12: 115,122,166 (GRCm39)	I70F	possibly damaging	Het
Kat7	A	G	11: 95,171,298 (GRCm39)	F469L	probably damaging	Het
Klk14	G	A	7: 43,341,501 (GRCm39)	C51Y	probably damaging	Het
Krt81	T	A	15: 101,359,193 (GRCm39)	M242L	probably benign	Het
Krtap6-1	A	G	16: 88,828,584 (GRCm39)		probably null	Het
Man2c1	A	G	9: 57,045,310 (GRCm39)	D473G	probably benign	Het
Mthfr-ps1	T	C	5: 78,622,436 (GRCm39)		noncoding transcript	Het
Nop53	A	T	7: 15,676,244 (GRCm39)	W152R	probably benign	Het
Or5p58	A	T	7: 107,694,591 (GRCm39)	M62K	probably damaging	Het
Or6y1	T	A	1: 174,277,162 (GRCm39)	S324R	unknown	Het
Or8s8	A	G	15: 98,354,878 (GRCm39)	E229G	probably benign	Het
Pcdh1	A	T	18: 38,331,358 (GRCm39)	N548K	probably damaging	Het
Pcdhga12	A	G	18: 37,899,467 (GRCm39)	I100V	probably benign	Het
Piezo2	T	C	18: 63,183,675 (GRCm39)	H1743R	probably benign	Het
Pkdrej	A	G	15: 85,700,515 (GRCm39)	V1807A	probably benign	Het
Rabl2	T	C	15: 89,474,582 (GRCm39)	M1V	probably null	Het
Rexo5	A	G	7: 119,426,621 (GRCm39)		probably benign	Het
Rfng	C	G	11: 120,674,772 (GRCm39)	G73R	probably benign	Het
Rps6ka4	A	G	19: 6,809,188 (GRCm39)	L459P	possibly damaging	Het
Samd11	T	A	4: 156,332,203 (GRCm39)	D536V	probably damaging	Het
Slc9a5	A	G	8: 106,084,032 (GRCm39)	T451A	possibly damaging	Het
Snapc1	T	A	12: 74,029,265 (GRCm39)	N349K	probably benign	Het
Sox1ot	A	G	8: 12,480,544 (GRCm39)		noncoding transcript	Het
Tmem178	C	T	17: 81,252,232 (GRCm39)	H39Y	possibly damaging	Het
Trav8n-2	A	T	14: 53,583,875 (GRCm39)	T111S	possibly damaging	Het
Ttn	T	A	2: 76,703,103 (GRCm39)		probably benign	Het
Ttn	T	C	2: 76,762,909 (GRCm39)	D3250G	probably damaging	Het
Ube2nl	T	A	7: 61,199,380 (GRCm39)		noncoding transcript	Het
Zkscan14	G	A	5: 145,132,985 (GRCm39)	T182I	possibly damaging	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
R0565:Vps25	UTSW	11	101,149,731 (GRCm39)	unclassified	probably benign
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'- GCCCTGATGATTCACTTGGG -3'
(R):5'- TGCCTACTGTGGGTAAAGGG -3'

Sequencing Primer
(F):5'- CCTGATGATTCACTTGGGGTTCC -3'
(R):5'- CCTACTGTGGGTAAAGGGAGGTG -3'

Posted On

2015-06-12