Mutagenetix > Incidental Mutation

Incidental Mutation 'R1817:Pgap1'

204461

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

039845-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.764) question?

Stock #

R1817 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

54512159-54596843 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 54575128 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Serine at position 265 (A265S)

Ref Sequence

ENSEMBL: ENSMUSP00000095346 (fasta)

Gene Model

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

AlphaFold

Q3UUQ7

Predicted Effect

probably benign
Transcript: ENSMUST00000097739
AA Change: A265S

PolyPhen 2 Score 0.151 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000095346
Gene: ENSMUSG00000073678
AA Change: A265S

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000185817

Meta Mutation Damage Score

0.0652

Coding Region Coverage

1x: 97.4%
3x: 96.9%
10x: 95.2%
20x: 91.9%

Validation Efficiency

95% (90/95)

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: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca6	A	T	11: 110,110,144 (GRCm39)	S600T	probably benign	Het
Acly	T	A	11: 100,386,717 (GRCm39)	Q615L	probably benign	Het
Adgrf1	C	A	17: 43,620,924 (GRCm39)	T387K	probably benign	Het
Afg3l1	G	T	8: 124,228,670 (GRCm39)	K745N	probably damaging	Het
Armc8	T	C	9: 99,418,312 (GRCm39)	T39A	possibly damaging	Het
Atm	C	A	9: 53,403,533 (GRCm39)		probably benign	Het
Babam2	A	G	5: 32,214,890 (GRCm39)	T324A	probably damaging	Het
Btd	C	A	14: 31,384,246 (GRCm39)	D77E	possibly damaging	Het
Cadm1	T	A	9: 47,740,668 (GRCm39)		probably benign	Het
Card11	A	T	5: 140,871,315 (GRCm39)	D729E	probably benign	Het
Ccni	G	T	5: 93,335,967 (GRCm39)	T144K	possibly damaging	Het
Ceacam23	C	T	7: 17,607,255 (GRCm39)		noncoding transcript	Het
Cecr2	A	G	6: 120,708,228 (GRCm39)	T77A	probably damaging	Het
Cgas	A	G	9: 78,341,593 (GRCm39)		probably null	Het
Cpsf7	T	C	19: 10,512,803 (GRCm39)	F296L	possibly damaging	Het
Cyfip1	C	A	7: 55,523,196 (GRCm39)	N70K	possibly damaging	Het
Cyp4a12b	A	G	4: 115,271,259 (GRCm39)		probably benign	Het
Ddx20	A	T	3: 105,585,896 (GRCm39)	Y816*	probably null	Het
Ddx59	A	G	1: 136,360,245 (GRCm39)	I420V	probably damaging	Het
Dgat1	T	A	15: 76,386,703 (GRCm39)	M445L	probably damaging	Het
Dnah5	T	A	15: 28,246,546 (GRCm39)	L628*	probably null	Het
Dnah7a	A	C	1: 53,598,307 (GRCm39)	D1409E	probably benign	Het
Dnmt1	T	C	9: 20,838,422 (GRCm39)	T215A	probably benign	Het
Dsg4	C	T	18: 20,604,302 (GRCm39)	T923M	probably damaging	Het
Enox1	A	G	14: 77,852,915 (GRCm39)	I394V	possibly damaging	Het
Esrp2	A	T	8: 106,861,250 (GRCm39)	M183K	probably damaging	Het
Fam171a1	C	T	2: 3,179,410 (GRCm39)	P79S	probably benign	Het
Fga	A	G	3: 82,939,082 (GRCm39)	T486A	probably benign	Het
Fkbp10	G	T	11: 100,306,715 (GRCm39)	A36S	probably benign	Het
Fnip1	A	G	11: 54,393,279 (GRCm39)	T572A	probably benign	Het
Fxn	A	C	19: 24,257,765 (GRCm39)		probably null	Het
Gaa	C	T	11: 119,175,324 (GRCm39)	Q901*	probably null	Het
Gabrg1	A	G	5: 70,911,594 (GRCm39)	M344T	probably benign	Het
Galnt7	C	T	8: 57,991,212 (GRCm39)	V433M	probably damaging	Het
Gin1	A	G	1: 97,712,951 (GRCm39)		probably null	Het
Hydin	A	C	8: 111,259,459 (GRCm39)	D2477A	probably benign	Het
Igsf6	T	C	7: 120,670,031 (GRCm39)	Y37C	probably damaging	Het
Il18rap	A	G	1: 40,570,687 (GRCm39)	I210V	probably benign	Het
Kif3a	T	C	11: 53,489,561 (GRCm39)	Y138H	probably damaging	Het
Klra17	A	G	6: 129,845,681 (GRCm39)		probably null	Het
Lcorl	A	T	5: 45,952,688 (GRCm39)	I55N	probably damaging	Het
Lrrc49	A	G	9: 60,510,059 (GRCm39)	S398P	possibly damaging	Het
Ltv1	A	G	10: 13,055,018 (GRCm39)	L384S	probably damaging	Het
Mageb3	A	T	2: 121,784,918 (GRCm39)	Y261*	probably null	Het
Mical3	T	G	6: 121,019,196 (GRCm39)	T9P	probably benign	Het
Myrip	C	T	9: 120,217,228 (GRCm39)	S49L	probably damaging	Het
Nrap	T	C	19: 56,372,487 (GRCm39)		probably benign	Het
Or2m12	T	C	16: 19,104,627 (GRCm39)	N289D	probably damaging	Het
Or4k5	A	G	14: 50,385,728 (GRCm39)	V201A	probably benign	Het
Otoa	A	T	7: 120,759,753 (GRCm39)		probably benign	Het
Pals2	T	G	6: 50,140,411 (GRCm39)	F144V	probably benign	Het
Parp11	T	A	6: 127,467,008 (GRCm39)	I133N	probably damaging	Het
Pcnx1	A	G	12: 81,965,416 (GRCm39)	T528A	probably benign	Het
Pde4c	A	G	8: 71,179,638 (GRCm39)	H63R	probably benign	Het
Pdpk1	T	C	17: 24,329,878 (GRCm39)	K53E	probably damaging	Het
Pdzd7	A	T	19: 45,024,615 (GRCm39)	M468K	probably damaging	Het
Perm1	C	A	4: 156,303,061 (GRCm39)	P535Q	possibly damaging	Het
Pik3c2a	A	T	7: 115,975,747 (GRCm39)		probably null	Het
Plxnd1	T	C	6: 115,957,562 (GRCm39)	T491A	possibly damaging	Het
Pms1	A	T	1: 53,246,128 (GRCm39)	D470E	probably benign	Het
Prf1	C	A	10: 61,138,762 (GRCm39)	T240N	probably damaging	Het
Prune2	A	G	19: 17,099,445 (GRCm39)	T1650A	probably benign	Het
Ptprf	A	G	4: 118,080,462 (GRCm39)	L1264P	probably benign	Het
Ptprs	A	G	17: 56,726,527 (GRCm39)	S948P	probably damaging	Het
Rapgef1	T	C	2: 29,576,268 (GRCm39)	V117A	probably damaging	Het
Rnf123	A	G	9: 107,940,125 (GRCm39)	V756A	probably benign	Het
Sez6l2	A	G	7: 126,566,291 (GRCm39)	E741G	probably damaging	Het
Shc3	A	T	13: 51,626,888 (GRCm39)	I125K	possibly damaging	Het
Smr3a	A	T	5: 88,155,917 (GRCm39)		probably benign	Het
Spef2	C	T	15: 9,584,194 (GRCm39)	E1624K	probably damaging	Het
St6gal1	A	T	16: 23,140,083 (GRCm39)	K85*	probably null	Het
Taf1b	T	G	12: 24,597,121 (GRCm39)	D353E	possibly damaging	Het
Tcp10b	C	T	17: 13,286,590 (GRCm39)	P180S	possibly damaging	Het
Tlr9	A	T	9: 106,102,142 (GRCm39)	M478L	probably benign	Het
Tpr	A	T	1: 150,295,654 (GRCm39)	E892D	probably damaging	Het
Trio	C	T	15: 27,742,581 (GRCm39)	W22*	probably null	Het
Usp14	A	G	18: 10,024,673 (GRCm39)	V8A	probably damaging	Het
Vmn2r19	A	T	6: 123,307,011 (GRCm39)	K506N	possibly damaging	Het
Vmn2r45	T	A	7: 8,475,372 (GRCm39)	N552I	probably damaging	Het
Vmn2r56	A	T	7: 12,449,542 (GRCm39)	M232K	probably benign	Het
Vps13b	T	A	15: 35,910,788 (GRCm39)	F3517L	possibly damaging	Het
Yif1a	C	T	19: 5,142,333 (GRCm39)	R247*	probably null	Het
Zbtb5	A	G	4: 44,993,767 (GRCm39)	V539A	probably benign	Het
Zfp180	G	A	7: 23,804,652 (GRCm39)	R357Q	probably damaging	Het
Zfp536	A	G	7: 37,268,042 (GRCm39)	L458P	probably damaging	Het
Zfp646	G	A	7: 127,482,292 (GRCm39)	G1490S	probably benign	Het
Zfp970	C	T	2: 177,167,976 (GRCm39)	H517Y	probably damaging	Het
Zranb3	A	T	1: 127,945,293 (GRCm39)		probably null	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
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
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

Predicted Primers

PCR Primer
(F):5'- GGTAAGTTCTACTATAGACAGTGTGG -3'
(R):5'- CATTGTTGCATGAAATGGCTTG -3'

Sequencing Primer
(F):5'- GCAACACACTACCAAATGGATTAGAG -3'
(R):5'- GCATGAAATGGCTTGTTTTTCAG -3'

Posted On

2014-06-23