Mutagenetix > Incidental Mutations

Incidental Mutation 'R0044:Pgap1'

32851

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

038338-MU

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.862) question?

Stock #

R0044 (G1)

Quality Score

225

Status

Validated (trace)

Chromosome

Chromosomal Location

54472994-54557684 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 54493368 bp

Zygosity

Heterozygous

Amino Acid Change

Leucine to Serine at position 664 (L664S)

Ref Sequence

ENSEMBL: ENSMUSP00000095346 (fasta)

Gene Model

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000097739
AA Change: L664S

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

SMART Domains

Protein: ENSMUSP00000095346
Gene: ENSMUSG00000073678
AA Change: L664S

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

0.3183

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.6%
20x: 93.6%

Validation Efficiency

100% (77/77)

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
6430571L13Rik	A	C	9: 107,342,499	R50S	probably damaging	Het
Actn2	G	T	13: 12,275,127	T176N	possibly damaging	Het
Adamts7	T	C	9: 90,171,588	V62A	possibly damaging	Het
Adcy2	A	G	13: 68,727,899	S495P	possibly damaging	Het
Agbl3	A	T	6: 34,799,899	M447L	probably damaging	Het
Asxl1	C	T	2: 153,400,209	T893I	probably benign	Het
Atp11b	T	A	3: 35,812,252	I400N	probably damaging	Het
Bpifb2	C	T	2: 153,882,679		probably benign	Het
Capn1	T	A	19: 6,014,343	Y42F	probably benign	Het
Cdk5rap2	A	T	4: 70,360,901	L190H	probably damaging	Het
Cfap54	T	C	10: 93,035,433	I594V	probably null	Het
Cpsf1	A	G	15: 76,599,553	V830A	probably benign	Het
Cyp2c70	T	A	19: 40,165,371	N258I	possibly damaging	Het
Dctn1	T	G	6: 83,191,134	Y386D	probably damaging	Het
Degs2	T	C	12: 108,692,154	N189D	probably damaging	Het
Dido1	C	T	2: 180,661,819	A1431T	probably damaging	Het
Diras1	G	T	10: 81,022,138	S93*	probably null	Het
E130308A19Rik	T	A	4: 59,690,290	H41Q	possibly damaging	Het
Ebf2	C	T	14: 67,310,968		probably benign	Het
Fcho2	A	G	13: 98,755,544		probably benign	Het
Gbe1	T	A	16: 70,561,132	Y681*	probably null	Het
Gm10036	A	C	18: 15,832,816	K8T	probably benign	Het
Herc1	T	A	9: 66,448,175	M2236K	probably benign	Het
Hmcn2	A	T	2: 31,412,508	Y2948F	probably damaging	Het
Jakmip2	A	T	18: 43,582,105	C119S	probably benign	Het
Kif1b	A	G	4: 149,263,601		probably benign	Het
Kif6	T	C	17: 49,832,256		probably benign	Het
Lpin1	A	T	12: 16,568,529		probably benign	Het
Lrp2	T	C	2: 69,527,555	I377V	probably benign	Het
Mavs	C	A	2: 131,242,024	T147N	probably damaging	Het
Mcoln2	C	T	3: 146,183,561	T374M	probably damaging	Het
Mreg	T	G	1: 72,162,375	T153P	probably damaging	Het
Naglu	T	C	11: 101,071,217	I172T	probably damaging	Het
Ogdhl	T	C	14: 32,339,328	V492A	possibly damaging	Het
Olfr1245	A	G	2: 89,575,630	I32T	possibly damaging	Het
Parvg	A	G	15: 84,337,882	E323G	probably benign	Het
Pgm2l1	A	G	7: 100,250,332	N51S	probably benign	Het
Pik3r6	A	G	11: 68,544,750	T609A	probably benign	Het
Plcb4	T	A	2: 135,971,856	V705E	probably damaging	Het
Plppr5	T	A	3: 117,671,889		probably null	Het
Prkg2	C	A	5: 98,973,130	D411Y	probably damaging	Het
Ptprd	A	G	4: 76,086,329	V63A	probably benign	Het
Ptprz1	T	A	6: 23,007,403	I1655N	probably damaging	Het
Raf1	T	A	6: 115,623,515	D10V	probably benign	Het
Rexo1	T	A	10: 80,544,378	Q928L	probably benign	Het
Rpl7l1	A	C	17: 46,778,530		probably null	Het
Rrm2b	A	G	15: 37,953,688	S39P	possibly damaging	Het
Scn5a	A	G	9: 119,492,047		probably null	Het
Sgtb	A	G	13: 104,129,260	T93A	probably benign	Het
Sigirr	G	T	7: 141,092,313		probably null	Het
Slc16a7	T	C	10: 125,228,082	D462G	probably benign	Het
Slc25a30	C	T	14: 75,769,649	A85T	probably benign	Het
Spata24	A	G	18: 35,656,834	S167P	probably damaging	Het
Spock3	C	T	8: 63,144,007	T115I	possibly damaging	Het
Srgap2	A	G	1: 131,319,551	I581T	possibly damaging	Het
Syn2	A	T	6: 115,135,147	M23L	unknown	Het
Synrg	G	A	11: 84,009,181	V839I	probably damaging	Het
Tmtc1	A	G	6: 148,412,829		probably benign	Het
Tnfaip3	C	A	10: 19,011,626	M50I	probably damaging	Het
Topbp1	T	A	9: 103,325,773	I721N	possibly damaging	Het
Ttc22	T	G	4: 106,636,806	V321G	probably benign	Het
Ttc25	A	T	11: 100,567,001	I477F	probably damaging	Het
Ubr2	A	G	17: 46,992,985		probably benign	Het
Ubr4	T	C	4: 139,437,058		probably benign	Het
Usp24	T	C	4: 106,412,084		probably benign	Het
Vmn2r100	A	T	17: 19,522,179	I272L	possibly damaging	Het
Vrtn	T	A	12: 84,648,605	L43H	probably damaging	Het
Wnk1	G	T	6: 120,037,149	R162S	probably damaging	Het
Xkr9	G	A	1: 13,684,062	W93*	probably null	Het
Zfp804b	G	T	5: 6,769,655	P1136H	probably damaging	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
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
R1817:Pgap1	UTSW	1	54535969	missense	probably benign	0.15
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'- AGTTGTGACAAGATTCCTGGTGGAATG -3'
(R):5'- GGATTCTGGTAGATGGCTAGACACCTC -3'

Sequencing Primer
(F):5'- ctggggattaggatagcacatac -3'
(R):5'- TAGATGGCTAGACACCTCTGATG -3'

Posted On

2013-05-09