Mutagenetix > Incidental Mutation

Incidental Mutation 'R0109:Pgap1'

17797

Institutional Source

Beutler Lab

Gene Symbol

Pgap1

Ensembl Gene

ENSMUSG00000073678

Gene Name

post-GPI attachment to proteins 1

Synonyms

9030223K07Rik, D230012E17Rik, oto, 5033403E17Rik, PGAP1

MMRRC Submission

038395-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.764) question?

Stock #

R0109 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

54512159-54596843 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 54533984 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Glutamic Acid at position 643 (V643E)

Ref Sequence

ENSEMBL: ENSMUSP00000095346 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000097739]

AlphaFold

Q3UUQ7

Predicted Effect

probably damaging
Transcript: ENSMUST00000097739
AA Change: V643E

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

SMART Domains

Protein: ENSMUSP00000095346
Gene: ENSMUSG00000073678
AA Change: V643E

Domain	Start	End	E-Value	Type
transmembrane domain	7	29	N/A	INTRINSIC
Pfam:PGAP1	82	302	7.2e-83	PFAM
transmembrane domain	597	619	N/A	INTRINSIC
transmembrane domain	678	700	N/A	INTRINSIC
transmembrane domain	737	759	N/A	INTRINSIC
transmembrane domain	819	838	N/A	INTRINSIC
low complexity region	854	866	N/A	INTRINSIC
low complexity region	871	884	N/A	INTRINSIC
transmembrane domain	902	921	N/A	INTRINSIC

Meta Mutation Damage Score

0.3337

Coding Region Coverage

1x: 90.6%
3x: 88.5%
10x: 83.8%
20x: 77.5%

Validation Efficiency

90% (95/106)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene functions early in the glycosylphosphatidylinositol (GPI) biosynthetic pathway, catalyzing the inositol deacylation of GPI. The encoded protein is required for the production of GPI that can attach to proteins, and this may be an important factor in the transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi. Defects in this gene are a cause of mental retardation, autosomal recessive 42. [provided by RefSeq, Mar 2016]
PHENOTYPE: Mutations in this gene result in a variety of forebrain, eye, jaw, craniofacial, ear, and vertebra defects that are background sensitive. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A2m	C	A	6: 121,636,262 (GRCm39)	H710Q	probably benign	Het
Abca14	A	T	7: 119,917,985 (GRCm39)	K1496*	probably null	Het
Anapc1	C	A	2: 128,476,613 (GRCm39)	R1335L	probably damaging	Het
Arhgef10l	A	T	4: 140,305,605 (GRCm39)	S203T	probably benign	Het
Astn1	C	T	1: 158,491,674 (GRCm39)	T41I	possibly damaging	Het
Atrnl1	T	A	19: 57,743,949 (GRCm39)	Y1184N	possibly damaging	Het
Avil	A	G	10: 126,849,513 (GRCm39)	N603S	probably benign	Het
Brca1	T	C	11: 101,421,916 (GRCm39)	D149G	possibly damaging	Het
Car14	C	A	3: 95,806,763 (GRCm39)	A234S	probably benign	Het
Cep164	A	C	9: 45,682,885 (GRCm39)	L935R	probably damaging	Het
Cps1	T	C	1: 67,268,577 (GRCm39)	V1435A	possibly damaging	Het
Csmd2	T	G	4: 128,438,536 (GRCm39)	S3038R	probably benign	Het
Cyp2j6	A	T	4: 96,406,394 (GRCm39)	I459N	probably damaging	Het
Cyth1	T	C	11: 118,073,132 (GRCm39)	E242G	probably damaging	Het
Dclk3	T	G	9: 111,296,738 (GRCm39)	L94R	possibly damaging	Het
Disp2	T	C	2: 118,622,297 (GRCm39)	S1010P	probably damaging	Het
Dlec1	G	A	9: 118,934,892 (GRCm39)	R145H	probably damaging	Het
Dsg3	T	C	18: 20,673,191 (GRCm39)	V954A	probably damaging	Het
Dync2h1	T	A	9: 7,111,487 (GRCm39)	D309V	probably damaging	Het
Fam13b	A	G	18: 34,584,361 (GRCm39)	I601T	probably benign	Het
Fgd5	T	A	6: 91,965,216 (GRCm39)	M325K	possibly damaging	Het
Frmpd1	A	T	4: 45,279,340 (GRCm39)	E688D	probably benign	Het
Gabrb1	C	T	5: 72,279,289 (GRCm39)		probably benign	Het
Gm6590	A	T	6: 130,461,869 (GRCm39)		noncoding transcript	Het
Gse1	T	A	8: 121,294,524 (GRCm39)	S284T	probably damaging	Het
Ipo13	C	T	4: 117,762,213 (GRCm39)	R387Q	possibly damaging	Het
Kctd16	A	G	18: 40,392,204 (GRCm39)	E264G	probably benign	Het
Krt73	A	T	15: 101,704,830 (GRCm39)	L352*	probably null	Het
Mapk15	A	T	15: 75,867,926 (GRCm39)	K153*	probably null	Het
Mcemp1	C	A	8: 3,717,055 (GRCm39)	Y65*	probably null	Het
Mcoln2	C	G	3: 145,881,473 (GRCm39)	R210G	probably damaging	Het
Miox	G	A	15: 89,219,784 (GRCm39)	V91I	probably benign	Het
Myh7b	A	G	2: 155,453,594 (GRCm39)	E6G	possibly damaging	Het
Ncapg	A	G	5: 45,851,090 (GRCm39)		probably null	Het
Nfyb	G	A	10: 82,590,836 (GRCm39)	A65V	possibly damaging	Het
Or4a69	A	G	2: 89,313,147 (GRCm39)	F111L	probably benign	Het
Or52d1	T	C	7: 103,755,812 (GRCm39)	S109P	probably damaging	Het
Or5b94	C	A	19: 12,652,224 (GRCm39)	F218L	probably benign	Het
Osbp2	A	C	11: 3,661,791 (GRCm39)	S754A	probably benign	Het
Pard3	C	T	8: 128,125,147 (GRCm39)	R712C	probably damaging	Het
Parp9	T	C	16: 35,768,711 (GRCm39)	I64T	probably damaging	Het
Pcm1	T	A	8: 41,710,974 (GRCm39)	H81Q	possibly damaging	Het
Pcnt	G	A	10: 76,225,030 (GRCm39)	P1825S	probably benign	Het
Pfkfb4	T	C	9: 108,827,957 (GRCm39)	V43A	probably benign	Het
Pip5k1a	T	C	3: 94,972,753 (GRCm39)	T433A	probably benign	Het
Pip5k1b	T	A	19: 24,356,411 (GRCm39)	M176L	probably benign	Het
Polg2	T	C	11: 106,667,958 (GRCm39)		probably benign	Het
Pomp	T	A	5: 147,812,323 (GRCm39)	H136Q	probably benign	Het
Ppfia4	A	T	1: 134,251,955 (GRCm39)		probably null	Het
Prdx2	G	A	8: 85,696,880 (GRCm39)	G4S	probably benign	Het
Rbm28	C	T	6: 29,160,104 (GRCm39)	G70D	probably benign	Het
Rdh10	T	A	1: 16,176,489 (GRCm39)	I83N	probably damaging	Het
Rin3	A	G	12: 102,279,340 (GRCm39)	I50V	possibly damaging	Het
Rnf122	T	C	8: 31,614,877 (GRCm39)		probably benign	Het
Sik2	A	G	9: 50,810,775 (GRCm39)	M447T	possibly damaging	Het
Sla2	A	G	2: 156,725,507 (GRCm39)		probably null	Het
Slc51a	T	A	16: 32,296,425 (GRCm39)	I192L	probably benign	Het
Sorcs1	T	C	19: 50,367,329 (GRCm39)		probably benign	Het
Spata16	T	A	3: 26,967,416 (GRCm39)	F389I	probably damaging	Het
Srebf1	G	A	11: 60,092,630 (GRCm39)	A793V	probably benign	Het
Tbc1d9b	T	C	11: 50,049,261 (GRCm39)	V736A	probably benign	Het
Tbx15	C	A	3: 99,259,182 (GRCm39)	T351N	possibly damaging	Het
Tep1	A	G	14: 51,089,373 (GRCm39)		probably null	Het
Tmed11	T	A	5: 108,925,278 (GRCm39)	D178V	probably damaging	Het
Traf7	A	G	17: 24,732,900 (GRCm39)	F110L	probably benign	Het
Ubqlnl	C	T	7: 103,799,399 (GRCm39)	V33M	probably damaging	Het
Vcan	A	T	13: 89,826,192 (GRCm39)		probably null	Het
Vmn1r194	A	G	13: 22,429,217 (GRCm39)	Y278C	probably damaging	Het
Vmn1r46	T	C	6: 89,954,044 (GRCm39)	F298L	probably benign	Het
Vps13b	A	G	15: 35,572,265 (GRCm39)	T961A	probably benign	Het
Wdr48	G	A	9: 119,747,634 (GRCm39)		probably benign	Het
Wwp1	G	A	4: 19,641,725 (GRCm39)		probably benign	Het
Zfp1001	A	T	2: 150,165,761 (GRCm39)		probably benign	Het
Zfp217	C	T	2: 169,957,382 (GRCm39)	A539T	probably benign	Het
Zfp839	G	A	12: 110,827,308 (GRCm39)	E400K	possibly damaging	Het

Other mutations in Pgap1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00846:Pgap1	APN	1	54,531,180 (GRCm39)	splice site	probably benign
IGL01111:Pgap1	APN	1	54,570,102 (GRCm39)	missense	probably benign	0.17
IGL01406:Pgap1	APN	1	54,572,573 (GRCm39)	splice site	probably null
IGL01592:Pgap1	APN	1	54,560,470 (GRCm39)	missense	probably damaging	1.00
IGL02005:Pgap1	APN	1	54,590,214 (GRCm39)	missense	probably damaging	0.99
IGL02026:Pgap1	APN	1	54,533,978 (GRCm39)	missense	probably benign	0.05
IGL02086:Pgap1	APN	1	54,587,147 (GRCm39)	missense	probably damaging	1.00
IGL02354:Pgap1	APN	1	54,551,975 (GRCm39)	missense	probably benign	0.02
IGL02361:Pgap1	APN	1	54,551,975 (GRCm39)	missense	probably benign	0.02
IGL02995:Pgap1	APN	1	54,532,509 (GRCm39)	missense	probably benign	0.19
IGL03012:Pgap1	APN	1	54,572,572 (GRCm39)	splice site	probably benign
R0044:Pgap1	UTSW	1	54,532,527 (GRCm39)	missense	probably damaging	1.00
R0109:Pgap1	UTSW	1	54,533,984 (GRCm39)	missense	probably damaging	1.00
R0241:Pgap1	UTSW	1	54,575,110 (GRCm39)	splice site	probably null
R0241:Pgap1	UTSW	1	54,575,110 (GRCm39)	splice site	probably null
R0352:Pgap1	UTSW	1	54,525,617 (GRCm39)	splice site	probably benign
R1297:Pgap1	UTSW	1	54,567,682 (GRCm39)	missense	possibly damaging	0.94
R1429:Pgap1	UTSW	1	54,534,020 (GRCm39)	missense	probably benign	0.01
R1465:Pgap1	UTSW	1	54,567,714 (GRCm39)	missense	probably benign	0.11
R1465:Pgap1	UTSW	1	54,567,714 (GRCm39)	missense	probably benign	0.11
R1542:Pgap1	UTSW	1	54,531,249 (GRCm39)	missense	probably benign	0.16
R1816:Pgap1	UTSW	1	54,531,216 (GRCm39)	missense	probably damaging	0.99
R1817:Pgap1	UTSW	1	54,575,128 (GRCm39)	missense	probably benign	0.15
R1905:Pgap1	UTSW	1	54,551,120 (GRCm39)	missense	probably benign	0.26
R2006:Pgap1	UTSW	1	54,590,220 (GRCm39)	missense	possibly damaging	0.76
R3551:Pgap1	UTSW	1	54,569,302 (GRCm39)	missense	possibly damaging	0.89
R3833:Pgap1	UTSW	1	54,596,624 (GRCm39)	missense	probably damaging	0.99
R3901:Pgap1	UTSW	1	54,532,507 (GRCm39)	missense	probably benign
R4487:Pgap1	UTSW	1	54,567,751 (GRCm39)	missense	probably benign	0.26
R4874:Pgap1	UTSW	1	54,569,296 (GRCm39)	missense	probably damaging	0.96
R5184:Pgap1	UTSW	1	54,521,015 (GRCm39)	missense	probably damaging	1.00
R6181:Pgap1	UTSW	1	54,551,936 (GRCm39)	missense	probably benign	0.05
R6212:Pgap1	UTSW	1	54,554,052 (GRCm39)	missense	probably damaging	0.99
R6269:Pgap1	UTSW	1	54,587,167 (GRCm39)	nonsense	probably null
R6525:Pgap1	UTSW	1	54,521,048 (GRCm39)	missense	probably benign	0.00
R6944:Pgap1	UTSW	1	54,569,320 (GRCm39)	missense	probably damaging	1.00
R7214:Pgap1	UTSW	1	54,582,220 (GRCm39)	missense	possibly damaging	0.47
R7256:Pgap1	UTSW	1	54,532,366 (GRCm39)	critical splice donor site	probably null
R7290:Pgap1	UTSW	1	54,587,225 (GRCm39)	missense	possibly damaging	0.45
R7356:Pgap1	UTSW	1	54,569,293 (GRCm39)	missense	probably benign	0.10
R7525:Pgap1	UTSW	1	54,570,081 (GRCm39)	missense	probably benign	0.26
R7602:Pgap1	UTSW	1	54,582,345 (GRCm39)	missense	probably damaging	1.00
R7897:Pgap1	UTSW	1	54,590,167 (GRCm39)	missense	probably damaging	1.00
R8278:Pgap1	UTSW	1	54,529,430 (GRCm39)	missense	probably benign
R9189:Pgap1	UTSW	1	54,519,908 (GRCm39)	missense	probably benign	0.31
R9238:Pgap1	UTSW	1	54,550,570 (GRCm39)	missense	probably benign
R9428:Pgap1	UTSW	1	54,575,206 (GRCm39)	missense	probably damaging	1.00
R9479:Pgap1	UTSW	1	54,582,275 (GRCm39)	nonsense	probably null
X0025:Pgap1	UTSW	1	54,521,029 (GRCm39)	missense	probably benign	0.26
X0060:Pgap1	UTSW	1	54,575,193 (GRCm39)	missense	probably damaging	1.00

Posted On

2013-01-31