Mutagenetix > Incidental Mutations

Incidental Mutation 'R1817:Pgap1'

204461

Institutional Source

Beutler Lab

Gene Symbol

Pgap1

Ensembl Gene

ENSMUSG00000073678

Gene Name

post-GPI attachment to proteins 1

Synonyms

PGAP1, D230012E17Rik, oto, 5033403E17Rik, 9030223K07Rik

MMRRC Submission

039845-MU

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.830) question?

Stock #

R1817 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

54472994-54557684 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 54535969 bp

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]

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: 110,219,318	S600T	probably benign	Het
Acly	T	A	11: 100,495,891	Q615L	probably benign	Het
Adgrf1	C	A	17: 43,310,033	T387K	probably benign	Het
Afg3l1	G	T	8: 123,501,931	K745N	probably damaging	Het
Armc8	T	C	9: 99,536,259	T39A	possibly damaging	Het
Atm	C	A	9: 53,492,233		probably benign	Het
Babam2	A	G	5: 32,057,546	T324A	probably damaging	Het
Btd	C	A	14: 31,662,289	D77E	possibly damaging	Het
Cadm1	T	A	9: 47,829,370		probably benign	Het
Card11	A	T	5: 140,885,560	D729E	probably benign	Het
Ccni	G	T	5: 93,188,108	T144K	possibly damaging	Het
Cecr2	A	G	6: 120,731,267	T77A	probably damaging	Het
Cpsf7	T	C	19: 10,535,439	F296L	possibly damaging	Het
Cyfip1	C	A	7: 55,873,448	N70K	possibly damaging	Het
Cyp4a12b	A	G	4: 115,414,062		probably benign	Het
Ddx20	A	T	3: 105,678,580	Y816*	probably null	Het
Ddx59	A	G	1: 136,432,507	I420V	probably damaging	Het
Dgat1	T	A	15: 76,502,503	M445L	probably damaging	Het
Dnah5	T	A	15: 28,246,400	L628*	probably null	Het
Dnah7a	A	C	1: 53,559,148	D1409E	probably benign	Het
Dnmt1	T	C	9: 20,927,126	T215A	probably benign	Het
Dsg4	C	T	18: 20,471,245	T923M	probably damaging	Het
Enox1	A	G	14: 77,615,475	I394V	possibly damaging	Het
Esrp2	A	T	8: 106,134,618	M183K	probably damaging	Het
Fam171a1	C	T	2: 3,178,373	P79S	probably benign	Het
Fga	A	G	3: 83,031,775	T486A	probably benign	Het
Fkbp10	G	T	11: 100,415,889	A36S	probably benign	Het
Fnip1	A	G	11: 54,502,453	T572A	probably benign	Het
Fxn	A	C	19: 24,280,401		probably null	Het
Gaa	C	T	11: 119,284,498	Q901*	probably null	Het
Gabrg1	A	G	5: 70,754,251	M344T	probably benign	Het
Galnt7	C	T	8: 57,538,178	V433M	probably damaging	Het
Gin1	A	G	1: 97,785,226		probably null	Het
Gm5155	C	T	7: 17,873,330		noncoding transcript	Het
Hydin	A	C	8: 110,532,827	D2477A	probably benign	Het
Igsf6	T	C	7: 121,070,808	Y37C	probably damaging	Het
Il18rap	A	G	1: 40,531,527	I210V	probably benign	Het
Kif3a	T	C	11: 53,598,734	Y138H	probably damaging	Het
Klra17	A	G	6: 129,868,718		probably null	Het
Lcorl	A	T	5: 45,795,346	I55N	probably damaging	Het
Lrrc49	A	G	9: 60,602,776	S398P	possibly damaging	Het
Ltv1	A	G	10: 13,179,274	L384S	probably damaging	Het
Mageb3	A	T	2: 121,954,437	Y261*	probably null	Het
Mb21d1	A	G	9: 78,434,311		probably null	Het
Mical3	T	G	6: 121,042,235	T9P	probably benign	Het
Mpp6	T	G	6: 50,163,431	F144V	probably benign	Het
Myrip	C	T	9: 120,388,162	S49L	probably damaging	Het
Nrap	T	C	19: 56,384,055		probably benign	Het
Olfr164	T	C	16: 19,285,877	N289D	probably damaging	Het
Olfr729	A	G	14: 50,148,271	V201A	probably benign	Het
Otoa	A	T	7: 121,160,530		probably benign	Het
Parp11	T	A	6: 127,490,045	I133N	probably damaging	Het
Pcnx	A	G	12: 81,918,642	T528A	probably benign	Het
Pde4c	A	G	8: 70,726,989	H63R	probably benign	Het
Pdpk1	T	C	17: 24,110,904	K53E	probably damaging	Het
Pdzd7	A	T	19: 45,036,176	M468K	probably damaging	Het
Perm1	C	A	4: 156,218,604	P535Q	possibly damaging	Het
Pik3c2a	A	T	7: 116,376,512		probably null	Het
Plxnd1	T	C	6: 115,980,601	T491A	possibly damaging	Het
Pms1	A	T	1: 53,206,969	D470E	probably benign	Het
Prf1	C	A	10: 61,302,983	T240N	probably damaging	Het
Prune2	A	G	19: 17,122,081	T1650A	probably benign	Het
Ptprf	A	G	4: 118,223,265	L1264P	probably benign	Het
Ptprs	A	G	17: 56,419,527	S948P	probably damaging	Het
Rapgef1	T	C	2: 29,686,256	V117A	probably damaging	Het
Rnf123	A	G	9: 108,062,926	V756A	probably benign	Het
Sez6l2	A	G	7: 126,967,119	E741G	probably damaging	Het
Shc3	A	T	13: 51,472,852	I125K	possibly damaging	Het
Smr3a	A	T	5: 88,008,058		probably benign	Het
Spef2	C	T	15: 9,584,108	E1624K	probably damaging	Het
St6gal1	A	T	16: 23,321,333	K85*	probably null	Het
Taf1b	T	G	12: 24,547,122	D353E	possibly damaging	Het
Tcp10b	C	T	17: 13,067,703	P180S	possibly damaging	Het
Tlr9	A	T	9: 106,224,943	M478L	probably benign	Het
Tpr	A	T	1: 150,419,903	E892D	probably damaging	Het
Trio	C	T	15: 27,742,495	W22*	probably null	Het
Usp14	A	G	18: 10,024,673	V8A	probably damaging	Het
Vmn2r19	A	T	6: 123,330,052	K506N	possibly damaging	Het
Vmn2r45	T	A	7: 8,472,373	N552I	probably damaging	Het
Vmn2r56	A	T	7: 12,715,615	M232K	probably benign	Het
Vps13b	T	A	15: 35,910,642	F3517L	possibly damaging	Het
Yif1a	C	T	19: 5,092,305	R247*	probably null	Het
Zbtb5	A	G	4: 44,993,767	V539A	probably benign	Het
Zfp180	G	A	7: 24,105,227	R357Q	probably damaging	Het
Zfp536	A	G	7: 37,568,617	L458P	probably damaging	Het
Zfp646	G	A	7: 127,883,120	G1490S	probably benign	Het
Zfp970	C	T	2: 177,476,183	H517Y	probably damaging	Het
Zranb3	A	T	1: 128,017,556		probably null	Het

Other mutations in Pgap1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00846:Pgap1	APN	1	54492021	splice site	probably benign
IGL01111:Pgap1	APN	1	54530943	missense	probably benign	0.17
IGL01406:Pgap1	APN	1	54533414	splice site	probably null
IGL01592:Pgap1	APN	1	54521311	missense	probably damaging	1.00
IGL02005:Pgap1	APN	1	54551055	missense	probably damaging	0.99
IGL02026:Pgap1	APN	1	54494819	missense	probably benign	0.05
IGL02086:Pgap1	APN	1	54547988	missense	probably damaging	1.00
IGL02354:Pgap1	APN	1	54512816	missense	probably benign	0.02
IGL02361:Pgap1	APN	1	54512816	missense	probably benign	0.02
IGL02995:Pgap1	APN	1	54493350	missense	probably benign	0.19
IGL03012:Pgap1	APN	1	54533413	splice site	probably benign
R0044:Pgap1	UTSW	1	54493368	missense	probably damaging	1.00
R0109:Pgap1	UTSW	1	54494825	missense	probably damaging	1.00
R0109:Pgap1	UTSW	1	54494825	missense	probably damaging	1.00
R0241:Pgap1	UTSW	1	54535951	splice site	probably null
R0241:Pgap1	UTSW	1	54535951	splice site	probably null
R0352:Pgap1	UTSW	1	54486458	splice site	probably benign
R1297:Pgap1	UTSW	1	54528523	missense	possibly damaging	0.94
R1429:Pgap1	UTSW	1	54494861	missense	probably benign	0.01
R1465:Pgap1	UTSW	1	54528555	missense	probably benign	0.11
R1465:Pgap1	UTSW	1	54528555	missense	probably benign	0.11
R1542:Pgap1	UTSW	1	54492090	missense	probably benign	0.16
R1816:Pgap1	UTSW	1	54492057	missense	probably damaging	0.99
R1905:Pgap1	UTSW	1	54511961	missense	probably benign	0.26
R2006:Pgap1	UTSW	1	54551061	missense	possibly damaging	0.76
R3551:Pgap1	UTSW	1	54530143	missense	possibly damaging	0.89
R3833:Pgap1	UTSW	1	54557465	missense	probably damaging	0.99
R3901:Pgap1	UTSW	1	54493348	missense	probably benign
R4487:Pgap1	UTSW	1	54528592	missense	probably benign	0.26
R4874:Pgap1	UTSW	1	54530137	missense	probably damaging	0.96
R5184:Pgap1	UTSW	1	54481856	missense	probably damaging	1.00
R6181:Pgap1	UTSW	1	54512777	missense	probably benign	0.05
R6212:Pgap1	UTSW	1	54514893	missense	probably damaging	0.99
R6269:Pgap1	UTSW	1	54548008	nonsense	probably null
R6525:Pgap1	UTSW	1	54481889	missense	probably benign	0.00
R6944:Pgap1	UTSW	1	54530161	missense	probably damaging	1.00
R7214:Pgap1	UTSW	1	54543061	missense	possibly damaging	0.47
R7256:Pgap1	UTSW	1	54493207	critical splice donor site	probably null
R7290:Pgap1	UTSW	1	54548066	missense	possibly damaging	0.45
R7356:Pgap1	UTSW	1	54530134	missense	probably benign	0.10
R7525:Pgap1	UTSW	1	54530922	missense	probably benign	0.26
R7602:Pgap1	UTSW	1	54543186	missense	probably damaging	1.00
R7897:Pgap1	UTSW	1	54551008	missense	probably damaging	1.00
R8278:Pgap1	UTSW	1	54490271	missense	probably benign
X0025:Pgap1	UTSW	1	54481870	missense	probably benign	0.26
X0060:Pgap1	UTSW	1	54536034	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