Mutagenetix > Incidental Mutation

Incidental Mutation 'R1933:Vps4a'

215585

Institutional Source

Beutler Lab

Gene Symbol

Vps4a

Ensembl Gene

ENSMUSG00000031913

Gene Name

vacuolar protein sorting 4A

Synonyms

4930589C15Rik

MMRRC Submission

039951-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1933 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

107757901-107772392 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 107771190 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 392 (V392A)

Ref Sequence

ENSEMBL: ENSMUSP00000034388 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000034388] [ENSMUST00000034391] [ENSMUST00000055316] [ENSMUST00000095517]

AlphaFold

Q8VEJ9

Predicted Effect

probably benign
Transcript: ENSMUST00000034388
AA Change: V392A

PolyPhen 2 Score 0.209 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000034388
Gene: ENSMUSG00000031913
AA Change: V392A

Domain	Start	End	E-Value	Type
MIT	2	80	2.02e-27	SMART
low complexity region	90	102	N/A	INTRINSIC
AAA	159	295	2.89e-22	SMART
Blast:AAA	329	358	8e-9	BLAST
Pfam:Vps4_C	374	434	1.9e-29	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000034391

SMART Domains

Protein: ENSMUSP00000034391
Gene: ENSMUSG00000031916

Domain	Start	End	E-Value	Type
low complexity region	10	21	N/A	INTRINSIC
Pfam:Dor1	56	394	7.6e-151	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000055316

SMART Domains

Protein: ENSMUSP00000138676
Gene: ENSMUSG00000078931

Domain	Start	End	E-Value	Type
Pfam:Pep_deformylase	52	222	2.3e-43	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000095517

SMART Domains

Protein: ENSMUSP00000093173
Gene: ENSMUSG00000031916

Domain	Start	End	E-Value	Type
low complexity region	10	21	N/A	INTRINSIC
Pfam:Dor1	56	394	7.6e-151	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132096

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144527

Predicted Effect

probably benign
Transcript: ENSMUST00000154271

Coding Region Coverage

1x: 97.5%
3x: 97.0%
10x: 95.7%
20x: 93.4%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of the AAA protein family (ATPases associated with diverse cellular activities), and is the homolog of the yeast Vps4 protein. In humans, two paralogs of the yeast protein have been identified. The former share a high degree of aa sequence similarity with each other, and also with yeast Vps4 and mouse Skd1 proteins. The mouse Skd1 (suppressor of K+ transport defect 1) has been shown to be really an yeast Vps4 ortholog. Functional studies indicate that both human paralogs associate with the endosomal compartments, and are involved in intracellular protein trafficking, similar to Vps4 protein in yeast. The gene encoding this paralog has been mapped to chromosome 16; the gene for the other resides on chromosome 18. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam25	A	T	8: 41,207,922 (GRCm39)	Y396F	probably benign	Het
Adra2a	T	A	19: 54,034,837 (GRCm39)	F64L	probably damaging	Het
Ankrd45	A	T	1: 160,978,870 (GRCm39)	N103I	probably damaging	Het
Arhgef7	C	A	8: 11,858,713 (GRCm39)		probably null	Het
Bsn	A	G	9: 107,993,643 (GRCm39)	V703A	possibly damaging	Het
Btaf1	T	A	19: 36,950,357 (GRCm39)	I529K	probably damaging	Het
Ccdc110	A	G	8: 46,396,287 (GRCm39)	N726S	probably damaging	Het
Ccdc78	T	A	17: 26,006,044 (GRCm39)	S71T	probably damaging	Het
Cct5	G	T	15: 31,591,154 (GRCm39)	Q516K	probably benign	Het
Cd300c2	A	T	11: 114,891,685 (GRCm39)	V63E	probably benign	Het
Cdh16	A	G	8: 105,344,595 (GRCm39)	V7A	possibly damaging	Het
Clec16a	T	C	16: 10,506,403 (GRCm39)	F710L	probably damaging	Het
Clpb	T	G	7: 101,428,418 (GRCm39)	F393V	probably damaging	Het
Commd9	G	A	2: 101,731,376 (GRCm39)	R187H	probably damaging	Het
Crx	T	A	7: 15,602,301 (GRCm39)	K126*	probably null	Het
Dcaf13	T	A	15: 39,001,483 (GRCm39)	Y264N	probably damaging	Het
Dnah12	T	A	14: 26,455,650 (GRCm39)	I791N	probably damaging	Het
Dpy19l1	A	T	9: 24,345,683 (GRCm39)	D456E	probably damaging	Het
Dscam	A	G	16: 96,394,414 (GRCm39)	S1963P	probably benign	Het
Efl1	C	T	7: 82,412,325 (GRCm39)	Q905*	probably null	Het
Farsa	T	C	8: 85,587,780 (GRCm39)	F104L	probably benign	Het
Fbxl19	C	A	7: 127,350,101 (GRCm39)	A231E	probably benign	Het
Fbxw19	A	T	9: 109,310,718 (GRCm39)	N401K	probably benign	Het
Foxp1	TTGCTGCTGCTGCTGCTGCTGCTGTTGCTGCTGCTGCTGTTGCTGCTGCTG	TTGCTGCTGCTGCTGCTGCTGTTGCTGCTGCTGCTGTTGCTGCTGCTG	6: 99,052,926 (GRCm39)		probably benign	Het
Frem3	A	G	8: 81,339,519 (GRCm39)	N604S	probably benign	Het
Gad1	T	G	2: 70,417,736 (GRCm39)	C312G	possibly damaging	Het
Garem2	G	T	5: 30,319,860 (GRCm39)	E441*	probably null	Het
Glra3	G	T	8: 56,393,942 (GRCm39)	A18S	probably benign	Het
Gm8206	A	T	14: 6,022,475 (GRCm38)	M8K	probably benign	Het
Gpr162	G	A	6: 124,838,410 (GRCm39)	S80F	probably damaging	Het
Grpr	C	A	X: 162,332,137 (GRCm39)	V53L	probably benign	Het
Il21	C	T	3: 37,286,635 (GRCm39)	R27H	probably benign	Het
Il21r	C	T	7: 125,228,153 (GRCm39)	T208I	possibly damaging	Het
Kcnab2	T	C	4: 152,520,323 (GRCm39)	T6A	possibly damaging	Het
Klra4	T	A	6: 130,042,207 (GRCm39)	Q20L	possibly damaging	Het
Lrrtm1	A	T	6: 77,221,949 (GRCm39)		probably null	Het
Lrrtm3	A	G	10: 63,924,292 (GRCm39)	F292L	possibly damaging	Het
Mpeg1	A	T	19: 12,440,011 (GRCm39)	K490*	probably null	Het
Myh14	C	T	7: 44,264,772 (GRCm39)	M1671I	probably benign	Het
Nebl	A	T	2: 17,380,103 (GRCm39)	M757K	probably damaging	Het
Or51m1	G	T	7: 103,578,337 (GRCm39)	M102I	probably damaging	Het
Or56b1b	A	C	7: 108,164,730 (GRCm39)	F91V	possibly damaging	Het
Or5aq1	T	A	2: 86,966,188 (GRCm39)	H159L	probably damaging	Het
Pkhd1l1	A	T	15: 44,404,280 (GRCm39)	H2303L	possibly damaging	Het
Podxl2	C	T	6: 88,826,587 (GRCm39)	V240M	probably benign	Het
Ppp2r5e	C	G	12: 75,516,341 (GRCm39)	A239P	probably damaging	Het
Prss53	T	C	7: 127,485,434 (GRCm39)	*553W	probably null	Het
Psma3	T	A	12: 71,031,468 (GRCm39)	M43K	probably benign	Het
Rad50	G	T	11: 53,570,888 (GRCm39)	T790K	probably benign	Het
Rasgrf1	G	T	9: 89,835,966 (GRCm39)	Q231H	probably damaging	Het
Rpn1	T	A	6: 88,070,841 (GRCm39)	V237E	probably damaging	Het
Scn10a	T	A	9: 119,439,064 (GRCm39)	M1601L	probably damaging	Het
Sema4f	G	T	6: 82,907,908 (GRCm39)	P180Q	probably damaging	Het
Serpinb5	A	G	1: 106,803,851 (GRCm39)	E8G	probably damaging	Het
Sgcg	C	T	14: 61,469,861 (GRCm39)	V167I	possibly damaging	Het
Slc25a13	C	T	6: 6,109,262 (GRCm39)	V367M	probably damaging	Het
Spata31	T	C	13: 65,068,424 (GRCm39)	S191P	probably benign	Het
Srbd1	A	G	17: 86,410,321 (GRCm39)	V537A	probably damaging	Het
Srgap1	G	T	10: 121,761,808 (GRCm39)	D113E	possibly damaging	Het
Srl	A	G	16: 4,310,214 (GRCm39)	I505T	probably damaging	Het
St14	G	A	9: 31,017,508 (GRCm39)	T226I	probably benign	Het
Stard9	T	A	2: 120,529,137 (GRCm39)	I1798N	possibly damaging	Het
Sugp1	A	G	8: 70,509,225 (GRCm39)	E166G	possibly damaging	Het
Susd1	A	T	4: 59,351,695 (GRCm39)	N455K	possibly damaging	Het
Sytl3	T	A	17: 7,000,445 (GRCm39)	V205E	probably damaging	Het
Tenm4	A	G	7: 96,544,533 (GRCm39)	Y2183C	probably damaging	Het
Tktl2	G	A	8: 66,964,999 (GRCm39)	V186M	probably damaging	Het
Tlcd3b	T	A	7: 126,426,844 (GRCm39)		probably null	Het
Tlr1	T	G	5: 65,082,781 (GRCm39)	T599P	possibly damaging	Het
Trpc6	G	A	9: 8,656,546 (GRCm39)	D658N	probably damaging	Het
Ttc39b	A	G	4: 83,150,957 (GRCm39)	V546A	possibly damaging	Het
Ube3c	T	C	5: 29,824,657 (GRCm39)	Y561H	probably damaging	Het
Vmn1r29	T	A	6: 58,284,405 (GRCm39)	S42T	probably benign	Het
Wdfy4	T	C	14: 32,855,301 (GRCm39)	E771G	probably benign	Het
Whrn	G	A	4: 63,333,876 (GRCm39)	Q415*	probably null	Het
Wnt5a	C	T	14: 28,233,802 (GRCm39)	P10L	probably benign	Het
Zfhx2	T	C	14: 55,312,695 (GRCm39)		probably benign	Het
Zfp451	T	C	1: 33,816,903 (GRCm39)	K132R	probably damaging	Het

Other mutations in Vps4a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00718:Vps4a	APN	8	107,769,258 (GRCm39)	missense	probably benign	0.00
IGL01123:Vps4a	APN	8	107,765,851 (GRCm39)	splice site	probably benign
IGL01538:Vps4a	APN	8	107,763,556 (GRCm39)	missense	probably benign	0.03
IGL02524:Vps4a	APN	8	107,763,383 (GRCm39)	splice site	probably benign
IGL02601:Vps4a	APN	8	107,769,693 (GRCm39)	missense	probably damaging	1.00
IGL02616:Vps4a	APN	8	107,768,909 (GRCm39)	missense	probably damaging	1.00
IGL03216:Vps4a	APN	8	107,763,335 (GRCm39)	missense	probably damaging	0.99
R0047:Vps4a	UTSW	8	107,763,333 (GRCm39)	missense	probably damaging	0.97
R0047:Vps4a	UTSW	8	107,763,333 (GRCm39)	missense	probably damaging	0.97
R0330:Vps4a	UTSW	8	107,769,698 (GRCm39)	missense	probably benign	0.01
R1384:Vps4a	UTSW	8	107,763,276 (GRCm39)	missense	possibly damaging	0.94
R7729:Vps4a	UTSW	8	107,767,529 (GRCm39)	missense	probably damaging	0.98
R8964:Vps4a	UTSW	8	107,771,686 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GAACCTCAGTACTCCCTTCAGC -3'
(R):5'- CAGGCCTTGGAATGATAGTGTC -3'

Sequencing Primer
(F):5'- GCCAGCCTTAGGTCCTGATGTAC -3'
(R):5'- GGCTTTTCTTCTTAAAGACCCTTAGG -3'

Posted On

2014-07-14