Mutagenetix > Incidental Mutation

Incidental Mutation 'R4676:Vipas39'

349594

Institutional Source

Beutler Lab

Gene Symbol

Vipas39

Ensembl Gene

ENSMUSG00000021038

Gene Name

VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog

Synonyms

MMRRC Submission

042013-MU

Accession Numbers

Is this an essential gene?

Possibly essential (E-score: 0.569) question?

Stock #

R4676 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

87238868-87266256 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 87241301 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Phenylalanine at position 445 (Y445F)

Ref Sequence

ENSEMBL: ENSMUSP00000137190 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021426] [ENSMUST00000072744] [ENSMUST00000179379] [ENSMUST00000221768] [ENSMUST00000222480]

AlphaFold

Q8BGQ1

Predicted Effect

probably damaging
Transcript: ENSMUST00000021426
AA Change: Y445F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000021426
Gene: ENSMUSG00000021038
AA Change: Y445F

Domain	Start	End	E-Value	Type
Pfam:Golgin_A5	24	470	4.3e-147	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000072744
AA Change: Y464F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000072527
Gene: ENSMUSG00000021038
AA Change: Y464F

Domain	Start	End	E-Value	Type
Pfam:Golgin_A5	24	489	3.7e-154	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000179379
AA Change: Y445F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000137190
Gene: ENSMUSG00000021038
AA Change: Y445F

Domain	Start	End	E-Value	Type
Pfam:Golgin_A5	24	470	4.3e-147	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000220858

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000221707

Predicted Effect

probably benign
Transcript: ENSMUST00000221768

Predicted Effect

probably benign
Transcript: ENSMUST00000222480

Meta Mutation Damage Score

0.5231

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.1%
20x: 94.8%

Validation Efficiency

98% (93/95)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein involved in the sorting of lysosomal proteins. Mutations in this gene are associated with ARCS2 (arthrogryposis, renal dysfunction, and cholestasis-2). Alternative splicing results in multiple transcript variants.[provided by RefSeq, Jul 2010]
PHENOTYPE: Mice homozygous for a conditional allele activated by an inducible cre exhibit dry and scaly skin, hair loss, and defects in tail tendon collagen I structure. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 84 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3110009E18Rik	T	A	1: 120,150,652	I13N	probably damaging	Het
Abcd3	T	A	3: 121,774,166	T409S	possibly damaging	Het
Acad12	C	A	5: 121,607,171	W317L	probably damaging	Het
Acap1	T	A	11: 69,889,468	M50L	probably benign	Het
Acvr1b	T	A	15: 101,202,986	V343E	probably damaging	Het
Adgb	C	A	10: 10,426,710	G371W	probably damaging	Het
AF529169	A	G	9: 89,601,553	V597A	probably damaging	Het
Akap9	A	G	5: 4,032,774	K1966R	probably damaging	Het
Akap9	C	T	5: 4,064,515	Q48*	probably null	Het
Ano10	T	C	9: 122,263,787	R159G	probably damaging	Het
Anxa7	T	C	14: 20,467,915	M128V	probably benign	Het
Arhgef40	C	A	14: 51,990,959	C554*	probably null	Het
Asna1	C	T	8: 85,018,873	A219T	probably benign	Het
Atf6	T	C	1: 170,787,410	Y538C	probably damaging	Het
Atp8b1	A	C	18: 64,538,678	D1091E	probably benign	Het
BC034090	A	G	1: 155,226,264	Y85H	possibly damaging	Het
BC067074	C	A	13: 113,368,807	L2157I	probably damaging	Het
BC067074	T	G	13: 113,368,808	L2157R	probably damaging	Het
Bcas2	A	G	3: 103,175,701		probably benign	Het
Bnc2	T	C	4: 84,292,819	N463D	probably damaging	Het
Capn7	A	T	14: 31,359,259	H411L	possibly damaging	Het
Cavin3	T	C	7: 105,481,113	E164G	probably damaging	Het
Ccdc191	T	C	16: 43,939,173		probably benign	Het
Ccdc88b	A	G	19: 6,853,000	V858A	probably benign	Het
Clcn3	A	G	8: 60,930,651		probably benign	Het
Commd6	T	C	14: 101,640,284		probably benign	Het
Cul3	G	A	1: 80,271,674	L561F	probably damaging	Het
Cyfip1	T	A	7: 55,875,013	I131N	probably damaging	Het
Dlgap3	T	A	4: 127,233,761	Y741N	probably damaging	Het
Dnah5	A	T	15: 28,295,260	I1380F	possibly damaging	Het
Dync1h1	G	T	12: 110,662,541	L4177F	probably damaging	Het
Ethe1	G	A	7: 24,607,894	V178M	probably damaging	Het
Flnc	A	T	6: 29,445,154		probably null	Het
Glt8d1	T	C	14: 31,006,692	F26L	probably benign	Het
Gm5493	T	A	17: 22,748,081	D63E	probably benign	Het
Gm9996	T	A	10: 29,143,838		probably benign	Het
Gnl2	T	G	4: 125,053,473	S629R	possibly damaging	Het
Gpbp1l1	T	C	4: 116,590,265	S381P	probably damaging	Het
Igsf10	A	C	3: 59,325,949	F1788V	probably benign	Het
Inpp5d	C	A	1: 87,715,142	P935Q	probably damaging	Het
Itch	A	C	2: 155,199,435	I468L	probably benign	Het
Itga5	A	T	15: 103,357,210	Y192N	probably damaging	Het
Itih3	T	A	14: 30,918,949	Q302L	probably null	Het
Itih3	T	A	14: 30,921,686	Q121L	possibly damaging	Het
Kctd17	T	A	15: 78,435,759		probably benign	Het
Lsm1	T	C	8: 25,793,689	L43P	probably damaging	Het
Magi3	A	T	3: 104,015,825	M1192K	probably benign	Het
Mecom	A	G	3: 30,268,668		probably benign	Het
Mtmr3	A	T	11: 4,527,855	F63Y	probably benign	Het
Naa16	A	G	14: 79,336,348		probably benign	Het
Neto1	A	T	18: 86,398,302	T45S	possibly damaging	Het
Nlrp4a	A	T	7: 26,450,229	R420S	probably damaging	Het
Nr1h4	T	C	10: 89,473,874	D317G	probably damaging	Het
Olfr1497	T	A	19: 13,795,474	I46F	possibly damaging	Het
Olfr1504	C	T	19: 13,887,401	D270N	probably damaging	Het
Olfr920	A	G	9: 38,755,659		probably benign	Het
Pde5a	A	T	3: 122,747,893	M11L	possibly damaging	Het
Plxnb1	G	A	9: 109,110,435	R1416Q	possibly damaging	Het
Polm	A	T	11: 5,835,749	Y141*	probably null	Het
Rxfp1	A	G	3: 79,705,668	F32L	probably damaging	Het
Scrt1	T	A	15: 76,521,668	D13V	possibly damaging	Het
Slc1a7	T	A	4: 107,977,674	V79E	possibly damaging	Het
Snurf	T	C	7: 59,995,522	Q48R	probably benign	Het
Srek1	T	C	13: 103,758,187		probably benign	Het
Stxbp5l	T	C	16: 37,255,884	S267G	probably damaging	Het
Taf5	C	T	19: 47,074,970	R320W	probably damaging	Het
Tars2	A	T	3: 95,753,091	N106K	probably damaging	Het
Tatdn3	A	T	1: 191,049,334	L207Q	probably damaging	Het
Tdrd6	T	C	17: 43,627,610	E849G	probably damaging	Het
Tedc2	T	C	17: 24,220,011	T111A	probably benign	Het
Tfg	T	A	16: 56,694,491		probably null	Het
Tgds	A	T	14: 118,116,231	S225T	probably benign	Het
Tnks2	T	A	19: 36,875,271	Y134*	probably null	Het
Trappc1	T	A	11: 69,325,530	V134D	probably damaging	Het
Ttc3	C	A	16: 94,442,761	P853Q	probably damaging	Het
Ttc7	C	A	17: 87,370,735		probably benign	Het
Ttf1	A	G	2: 29,074,594	S643G	probably damaging	Het
Tubgcp3	A	T	8: 12,650,171	S338T	probably damaging	Het
Ugt1a6a	T	C	1: 88,139,285	I271T	possibly damaging	Het
Vmn1r31	A	C	6: 58,472,013	I289S	probably damaging	Het
Wdr92	T	C	11: 17,229,794	V265A	probably benign	Het
Zfp112	A	G	7: 24,126,260	E551G	probably damaging	Het
Zfp397	T	A	18: 23,960,797	Y446*	probably null	Het
Zfp442	A	T	2: 150,409,606	H124Q	probably damaging	Het

Other mutations in Vipas39

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01413:Vipas39	APN	12	87249397	missense	probably benign	0.03
IGL01418:Vipas39	APN	12	87249397	missense	probably benign	0.03
IGL02026:Vipas39	APN	12	87251709	splice site	probably benign
IGL03089:Vipas39	APN	12	87253254	missense	probably damaging	1.00
R0173:Vipas39	UTSW	12	87250511	splice site	probably benign
R0909:Vipas39	UTSW	12	87241331	missense	probably benign	0.21
R1505:Vipas39	UTSW	12	87246160	missense	probably damaging	1.00
R2897:Vipas39	UTSW	12	87242523	missense	possibly damaging	0.78
R2968:Vipas39	UTSW	12	87242571	missense	probably benign	0.45
R2969:Vipas39	UTSW	12	87242571	missense	probably benign	0.45
R2970:Vipas39	UTSW	12	87242571	missense	probably benign	0.45
R4622:Vipas39	UTSW	12	87244543	missense	probably damaging	1.00
R5181:Vipas39	UTSW	12	87239827	missense	probably damaging	1.00
R5188:Vipas39	UTSW	12	87254247	missense	probably benign	0.21
R5881:Vipas39	UTSW	12	87251807	nonsense	probably null
R6080:Vipas39	UTSW	12	87241953	missense	probably damaging	1.00
R6425:Vipas39	UTSW	12	87241289	missense	probably damaging	0.98
R6896:Vipas39	UTSW	12	87242571	missense	probably benign	0.45
R7438:Vipas39	UTSW	12	87241931	splice site	probably null
R7538:Vipas39	UTSW	12	87263903	critical splice donor site	probably null
R8436:Vipas39	UTSW	12	87257417	missense	probably damaging	0.99
R8919:Vipas39	UTSW	12	87259084	nonsense	probably null
R9174:Vipas39	UTSW	12	87259111	missense	possibly damaging	0.89
R9460:Vipas39	UTSW	12	87241247	missense	probably damaging	1.00
R9671:Vipas39	UTSW	12	87246211	missense	probably benign	0.13

Predicted Primers

PCR Primer
(F):5'- ACAGGTGGGTCTTGTATCCATG -3'
(R):5'- GGTCTCCGAATTGAATTCTCAGC -3'

Sequencing Primer
(F):5'- GTATCCATGTGGCTCAGCTCAG -3'
(R):5'- GGTGGCTCACAACCATCTGTAATG -3'

Posted On

2015-10-08