Mutagenetix > Incidental Mutation

Incidental Mutation 'R7078:Pdcd6ip'

549358

Institutional Source

Beutler Lab

Gene Symbol

Pdcd6ip

Ensembl Gene

ENSMUSG00000032504

Gene Name

programmed cell death 6 interacting protein

Synonyms

AIP1, Alix

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7078 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

113480812-113537327 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 113488953 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 694 (N694S)

Ref Sequence

ENSEMBL: ENSMUSP00000107492 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000035086] [ENSMUST00000111861]

AlphaFold

Q9WU78

Predicted Effect

probably benign
Transcript: ENSMUST00000035086
AA Change: N689S

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000035086
Gene: ENSMUSG00000032504
AA Change: N689S

Domain	Start	End	E-Value	Type
BRO1	3	382	1.99e-160	SMART
Pfam:ALIX_LYPXL_bnd	408	702	3.6e-91	PFAM
low complexity region	731	812	N/A	INTRINSIC
Blast:BRO1	813	839	2e-11	BLAST
low complexity region	840	869	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000111861
AA Change: N694S

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000107492
Gene: ENSMUSG00000032504
AA Change: N694S

Domain	Start	End	E-Value	Type
BRO1	3	387	3.46e-160	SMART
Pfam:ALIX_LYPXL_bnd	417	706	8.8e-96	PFAM
low complexity region	736	817	N/A	INTRINSIC
Blast:BRO1	818	844	2e-11	BLAST
low complexity region	845	874	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that functions within the ESCRT pathway in the abscission stage of cytokinesis, in intralumenal endosomal vesicle formation, and in enveloped virus budding. Studies using mouse cells have shown that overexpression of this protein can block apoptosis. In addition, the product of this gene binds to the product of the PDCD6 gene, a protein required for apoptosis, in a calcium-dependent manner. This gene product also binds to endophilins, proteins that regulate membrane shape during endocytosis. Overexpression of this gene product and endophilins results in cytoplasmic vacuolization, which may be partly responsible for the protection against cell death. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. Related pseudogenes have been identified on chromosome 15. [provided by RefSeq, Jan 2012]
PHENOTYPE: Mice homozygous for a knock-out allele show decreased body and brain size and exhibit structural defects in the epithelium of the choroid plexus and in the brain ependyma that culminate in excessive cell extrusion, enlargement of the lateral ventricles, and hydrocephalus. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 91 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acaca	G	A	11: 84,154,138 (GRCm39)	R953Q	possibly damaging	Het
Aldh1a1	A	T	19: 20,579,434 (GRCm39)	H20L	probably benign	Het
Ankrd52	T	A	10: 128,219,526 (GRCm39)	C487S	probably benign	Het
Ap1s3	T	C	1: 79,602,845 (GRCm39)	E54G	probably benign	Het
Arglu1	A	C	8: 8,717,361 (GRCm39)	M236R	probably benign	Het
Baz1b	T	A	5: 135,246,293 (GRCm39)	F581I	probably benign	Het
Bbox1	T	G	2: 110,122,884 (GRCm39)	D135A	probably benign	Het
Bcl2l14	T	A	6: 134,400,786 (GRCm39)	V69E	probably damaging	Het
Brinp3	C	T	1: 146,390,627 (GRCm39)	Q58*	probably null	Het
Ccnb1ip1	T	A	14: 51,029,724 (GRCm39)	K113*	probably null	Het
Cep128	T	C	12: 91,200,878 (GRCm39)	I830M	probably damaging	Het
Ces2f	C	T	8: 105,681,284 (GRCm39)	T541I	probably damaging	Het
Chsy3	C	A	18: 59,309,149 (GRCm39)	P134Q	possibly damaging	Het
Cobl	T	G	11: 12,328,271 (GRCm39)	T112P	probably damaging	Het
Cplane2	A	T	4: 140,947,159 (GRCm39)	Y180F	probably benign	Het
Dcc	T	A	18: 71,680,469 (GRCm39)	K589I	probably benign	Het
Depdc1b	T	A	13: 108,523,505 (GRCm39)	I460K	possibly damaging	Het
Dlst	T	C	12: 85,157,705 (GRCm39)	F12S	probably benign	Het
Dnah1	G	C	14: 31,019,067 (GRCm39)	F1342L	probably damaging	Het
Dtnb	A	G	12: 3,798,480 (GRCm39)	Q438R	possibly damaging	Het
Dusp4	C	A	8: 35,275,065 (GRCm39)	S61R	probably damaging	Het
E130308A19Rik	A	G	4: 59,737,688 (GRCm39)	Y433C	probably damaging	Het
Ebf2	T	C	14: 67,661,407 (GRCm39)	S512P	probably benign	Het
Elapor2	A	G	5: 9,460,709 (GRCm39)	N210S	probably benign	Het
Eya1	C	T	1: 14,301,636 (GRCm39)		probably null	Het
Fsd1	G	A	17: 56,300,876 (GRCm39)	R245H	probably damaging	Het
Fzr1	T	A	10: 81,204,463 (GRCm39)	D379V	probably damaging	Het
Gk2	T	A	5: 97,604,195 (GRCm39)	E214D	probably benign	Het
Gm10837	C	G	14: 122,728,142 (GRCm39)	A6G	unknown	Het
Gmnc	A	T	16: 26,779,272 (GRCm39)	V251E	probably benign	Het
Golga3	A	G	5: 110,340,953 (GRCm39)	Q549R	probably damaging	Het
Gsdmd	T	G	15: 75,736,204 (GRCm39)	V111G	probably damaging	Het
Gtf3c1	T	C	7: 125,244,914 (GRCm39)	T1707A	possibly damaging	Het
Gucy2c	C	T	6: 136,674,937 (GRCm39)	V1049M	probably benign	Het
Gucy2g	A	G	19: 55,229,583 (GRCm39)	V29A	probably damaging	Het
Hecw1	A	T	13: 14,609,044 (GRCm39)	M1K	probably null	Het
Hmcn1	T	C	1: 150,736,118 (GRCm39)	D117G	probably damaging	Het
Ifnab	T	A	4: 88,609,350 (GRCm39)	T39S	possibly damaging	Het
Lcorl	A	G	5: 45,904,566 (GRCm39)	Y171H	probably damaging	Het
Ly6g6c	C	T	17: 35,288,437 (GRCm39)	P103L	probably damaging	Het
Macf1	T	G	4: 123,325,936 (GRCm39)	E5189A	probably damaging	Het
Mapkap1	A	G	2: 34,453,151 (GRCm39)	E348G	probably damaging	Het
Med25	G	T	7: 44,534,325 (GRCm39)	A280D	probably damaging	Het
Mep1b	C	A	18: 21,233,108 (GRCm39)	A703E	probably benign	Het
Morn5	T	A	2: 35,944,990 (GRCm39)	N71K	probably benign	Het
Mtmr10	T	A	7: 63,970,375 (GRCm39)	Y373N	possibly damaging	Het
Myo1d	C	T	11: 80,565,460 (GRCm39)	E426K	probably damaging	Het
Ncbp1	G	C	4: 46,155,756 (GRCm39)	V302L	probably benign	Het
Notch4	A	G	17: 34,801,520 (GRCm39)	T1123A	possibly damaging	Het
Nudt18	T	A	14: 70,816,452 (GRCm39)	M88K	possibly damaging	Het
Or12k8	A	G	2: 36,975,608 (GRCm39)	S51P	possibly damaging	Het
Or5b100-ps1	A	T	19: 12,994,097 (GRCm39)	D170V	possibly damaging	Het
Or6d12	T	A	6: 116,493,632 (GRCm39)	L298Q	probably damaging	Het
Or8g4	A	T	9: 39,661,787 (GRCm39)	Y35F	possibly damaging	Het
Pecam1	T	A	11: 106,579,773 (GRCm39)	T430S	probably benign	Het
Plaa	T	G	4: 94,462,288 (GRCm39)	T530P	probably benign	Het
Ppfia3	G	T	7: 45,010,019 (GRCm39)	Q95K	probably damaging	Het
Ppp4r2	T	C	6: 100,843,274 (GRCm39)	S331P	probably benign	Het
Prg4	T	C	1: 150,334,014 (GRCm39)	T117A	possibly damaging	Het
Prrc2b	A	T	2: 32,103,531 (GRCm39)	D1003V	probably benign	Het
Ptk2	G	A	15: 73,093,658 (GRCm39)	P854S	possibly damaging	Het
Rasef	T	C	4: 73,698,626 (GRCm39)	I12V	probably benign	Het
Robo2	T	G	16: 74,149,504 (GRCm39)	Y108S	probably damaging	Het
Rp1	T	A	1: 4,277,014 (GRCm39)	E762V	unknown	Het
Rsrc1	T	C	3: 66,901,987 (GRCm39)	S46P	unknown	Het
Rttn	A	T	18: 89,027,546 (GRCm39)	T554S	probably benign	Het
Sall3	C	T	18: 81,017,314 (GRCm39)	V205M	probably damaging	Het
Scn3a	C	A	2: 65,327,944 (GRCm39)	V849L	probably damaging	Het
Sec23a	A	G	12: 59,039,069 (GRCm39)	C277R	probably benign	Het
Sf3b3	C	T	8: 111,539,639 (GRCm39)	A1075T	possibly damaging	Het
Sfxn5	T	C	6: 85,309,366 (GRCm39)	D113G	unknown	Het
Slc22a22	C	T	15: 57,126,876 (GRCm39)	M64I	probably benign	Het
Slc5a11	C	T	7: 122,857,669 (GRCm39)	P253S	probably damaging	Het
Smarcd3	A	G	5: 24,798,067 (GRCm39)	F449S	probably damaging	Het
Sspo	C	T	6: 48,437,313 (GRCm39)	T1357M	probably damaging	Het
Styx	C	T	14: 45,609,873 (GRCm39)	T179I	probably benign	Het
Syt7	A	T	19: 10,412,963 (GRCm39)	T297S	probably benign	Het
Tbx19	T	A	1: 164,988,135 (GRCm39)		probably benign	Het
Tg	T	A	15: 66,545,392 (GRCm39)	V149E	probably damaging	Het
Tgfbr3l	T	A	8: 4,299,238 (GRCm39)	L35Q	probably damaging	Het
Tmem161b	C	A	13: 84,370,537 (GRCm39)		probably benign	Het
Tmem219	T	A	7: 126,490,975 (GRCm39)	T161S	probably damaging	Het
Tox2	T	A	2: 163,162,501 (GRCm39)	L68H		Het
Trim5	T	A	7: 103,927,681 (GRCm39)	D153V	possibly damaging	Het
Ttn	T	C	2: 76,580,651 (GRCm39)	Y23414C	probably damaging	Het
Ttn	A	T	2: 76,582,153 (GRCm39)	N22913K	probably damaging	Het
Ubr2	A	C	17: 47,266,779 (GRCm39)	M1124R	possibly damaging	Het
Vmn2r75	A	G	7: 85,815,568 (GRCm39)	S99P	probably damaging	Het
Wdr83	T	C	8: 85,802,680 (GRCm39)	D219G	probably damaging	Het
Wdr90	C	T	17: 26,068,623 (GRCm39)	V1285M	probably damaging	Het
Zmynd15	A	T	11: 70,351,581 (GRCm39)	L62F	probably damaging	Het

Other mutations in Pdcd6ip

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00087:Pdcd6ip	APN	9	113,526,586 (GRCm39)	missense	possibly damaging	0.89
IGL00814:Pdcd6ip	APN	9	113,516,721 (GRCm39)	missense	probably damaging	0.97
IGL01092:Pdcd6ip	APN	9	113,509,249 (GRCm39)	splice site	probably benign
IGL01621:Pdcd6ip	APN	9	113,514,490 (GRCm39)	missense	probably benign	0.03
IGL01781:Pdcd6ip	APN	9	113,520,566 (GRCm39)	missense	probably damaging	1.00
IGL02158:Pdcd6ip	APN	9	113,509,121 (GRCm39)	nonsense	probably null
IGL03136:Pdcd6ip	APN	9	113,520,567 (GRCm39)	missense	probably damaging	1.00
IGL03137:Pdcd6ip	APN	9	113,486,213 (GRCm39)	missense	possibly damaging	0.69
IGL03246:Pdcd6ip	APN	9	113,507,485 (GRCm39)	missense	possibly damaging	0.93
R0230:Pdcd6ip	UTSW	9	113,514,361 (GRCm39)	splice site	probably benign
R0284:Pdcd6ip	UTSW	9	113,491,572 (GRCm39)	missense	probably damaging	1.00
R0862:Pdcd6ip	UTSW	9	113,503,578 (GRCm39)	splice site	probably benign
R0864:Pdcd6ip	UTSW	9	113,503,578 (GRCm39)	splice site	probably benign
R1025:Pdcd6ip	UTSW	9	113,491,354 (GRCm39)	missense	probably damaging	1.00
R1687:Pdcd6ip	UTSW	9	113,529,087 (GRCm39)	missense	probably damaging	1.00
R1699:Pdcd6ip	UTSW	9	113,507,422 (GRCm39)	missense	probably damaging	1.00
R1957:Pdcd6ip	UTSW	9	113,537,090 (GRCm39)	missense	probably damaging	1.00
R2317:Pdcd6ip	UTSW	9	113,501,842 (GRCm39)	missense	probably benign	0.03
R2698:Pdcd6ip	UTSW	9	113,503,575 (GRCm39)	splice site	probably null
R4182:Pdcd6ip	UTSW	9	113,529,078 (GRCm39)	missense	probably benign	0.00
R5154:Pdcd6ip	UTSW	9	113,520,610 (GRCm39)	missense	probably damaging	1.00
R5229:Pdcd6ip	UTSW	9	113,507,401 (GRCm39)	missense	probably damaging	0.99
R5391:Pdcd6ip	UTSW	9	113,520,586 (GRCm39)	missense	probably damaging	1.00
R5972:Pdcd6ip	UTSW	9	113,491,366 (GRCm39)	missense	probably benign	0.07
R6149:Pdcd6ip	UTSW	9	113,488,939 (GRCm39)	missense	probably benign	0.03
R6406:Pdcd6ip	UTSW	9	113,503,412 (GRCm39)	missense	possibly damaging	0.81
R6514:Pdcd6ip	UTSW	9	113,518,762 (GRCm39)	missense	probably benign	0.43
R6869:Pdcd6ip	UTSW	9	113,484,174 (GRCm39)	missense	unknown
R6888:Pdcd6ip	UTSW	9	113,500,905 (GRCm39)	missense	probably benign	0.04
R7683:Pdcd6ip	UTSW	9	113,516,763 (GRCm39)	missense	probably damaging	1.00
R8260:Pdcd6ip	UTSW	9	113,501,865 (GRCm39)	missense	probably benign	0.05
R8376:Pdcd6ip	UTSW	9	113,518,684 (GRCm39)	missense	probably damaging	1.00
R8495:Pdcd6ip	UTSW	9	113,518,775 (GRCm39)	missense	probably benign	0.23
R8926:Pdcd6ip	UTSW	9	113,514,493 (GRCm39)	missense	probably benign	0.23
R9080:Pdcd6ip	UTSW	9	113,520,624 (GRCm39)	missense	probably damaging	0.96
R9260:Pdcd6ip	UTSW	9	113,526,572 (GRCm39)	critical splice donor site	probably null
R9315:Pdcd6ip	UTSW	9	113,488,921 (GRCm39)	missense	possibly damaging	0.50
R9542:Pdcd6ip	UTSW	9	113,520,589 (GRCm39)	missense	probably damaging	1.00
R9546:Pdcd6ip	UTSW	9	113,484,174 (GRCm39)	missense	unknown
R9547:Pdcd6ip	UTSW	9	113,484,174 (GRCm39)	missense	unknown
Z1177:Pdcd6ip	UTSW	9	113,514,437 (GRCm39)	missense	possibly damaging	0.95

Predicted Primers

PCR Primer
(F):5'- ATCAAGGCGCCCTATGACTC -3'
(R):5'- AGTGTCAGTGACCAATCTTAGGAC -3'

Sequencing Primer
(F):5'- GCCCTATGACTCTGAGACGTC -3'
(R):5'- GCTACTCGACAGATTGTATGAATGC -3'

Posted On

2019-05-15