Mutagenetix > Incidental Mutation

Incidental Mutation 'R1905:Pgap1'

214251

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

039924-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.764) question?

Stock #

R1905 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

54512159-54596843 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 54551120 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Arginine at position 520 (I520R)

Ref Sequence

ENSEMBL: ENSMUSP00000095346 (fasta)

Gene Model

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

AlphaFold

Q3UUQ7

Predicted Effect

probably benign
Transcript: ENSMUST00000097739
AA Change: I520R

PolyPhen 2 Score 0.262 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000095346
Gene: ENSMUSG00000073678
AA Change: I520R

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

0.1243

Coding Region Coverage

1x: 97.5%
3x: 97.0%
10x: 95.5%
20x: 93.1%

Validation Efficiency

99% (90/91)

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: 89 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4833420G17Rik	G	T	13: 119,606,216 (GRCm39)	V153L	possibly damaging	Het
Adamts17	T	A	7: 66,697,220 (GRCm39)	C631*	probably null	Het
Adamts19	A	G	18: 59,166,017 (GRCm39)	R1070G	possibly damaging	Het
Aldh1a1	A	G	19: 20,595,362 (GRCm39)	E97G	probably damaging	Het
Bola2	T	A	7: 126,295,410 (GRCm39)	V40E	probably damaging	Het
Ccar1	A	G	10: 62,612,437 (GRCm39)	S243P	possibly damaging	Het
Cd80	A	T	16: 38,294,539 (GRCm39)	I141F	probably damaging	Het
Ceacam23	T	A	7: 17,607,477 (GRCm39)		noncoding transcript	Het
Chn2	T	C	6: 54,263,106 (GRCm39)	C92R	probably damaging	Het
Ciao2a	A	G	9: 66,039,929 (GRCm39)	K82R	probably benign	Het
Clk1	A	T	1: 58,461,101 (GRCm39)		probably benign	Het
Clock	T	C	5: 76,414,735 (GRCm39)		probably benign	Het
Cntnap3	A	G	13: 65,051,578 (GRCm39)	V26A	probably benign	Het
Csf3r	A	T	4: 125,936,538 (GRCm39)	K651N	probably benign	Het
Cul4a	T	C	8: 13,183,171 (GRCm39)	M322T	probably benign	Het
Cx3cl1	A	G	8: 95,506,687 (GRCm39)	T231A	probably benign	Het
Cyp2c68	A	T	19: 39,724,026 (GRCm39)	C213S	probably benign	Het
Dhx16	T	G	17: 36,199,247 (GRCm39)	S814A	probably benign	Het
Dnah1	T	C	14: 30,986,587 (GRCm39)	I3659V	probably benign	Het
Dock6	A	T	9: 21,740,870 (GRCm39)	V906D	probably benign	Het
Ep400	G	A	5: 110,818,814 (GRCm39)	T2738I	probably damaging	Het
Erbb4	A	T	1: 68,114,569 (GRCm39)		probably benign	Het
Fam135b	C	T	15: 71,404,836 (GRCm39)	R70H	probably damaging	Het
Fam13a	T	C	6: 58,930,475 (GRCm39)	Q479R	probably damaging	Het
Fcgr4	A	T	1: 170,856,874 (GRCm39)	Q247L	probably damaging	Het
Flnc	T	A	6: 29,459,459 (GRCm39)	C2520S	probably damaging	Het
Foxn1	A	G	11: 78,262,636 (GRCm39)		probably null	Het
Fsip2	C	T	2: 82,813,772 (GRCm39)	P3364S	possibly damaging	Het
Fzd8	C	T	18: 9,213,803 (GRCm39)	T295I	probably damaging	Het
Gm4744	G	A	6: 40,928,736 (GRCm39)		probably benign	Het
Gm4871	G	T	5: 144,966,859 (GRCm39)	A208D	probably damaging	Het
Gm527	A	G	12: 64,967,797 (GRCm39)	N73S	possibly damaging	Het
Gm5414	T	C	15: 101,533,075 (GRCm39)	I451V	probably damaging	Het
Golm1	A	T	13: 59,790,065 (GRCm39)	V245E	probably benign	Het
Grik1	A	T	16: 87,693,754 (GRCm39)	Y879*	probably null	Het
Grn	C	A	11: 102,327,276 (GRCm39)	P241Q	probably damaging	Het
H2-T7	T	C	17: 36,453,833 (GRCm39)		noncoding transcript	Het
Hjurp	T	C	1: 88,194,338 (GRCm39)	E190G	probably benign	Het
Hmcn1	A	C	1: 150,868,606 (GRCm39)	I66S	probably damaging	Het
Hykk	T	A	9: 54,853,667 (GRCm39)	Y330N	probably benign	Het
Khdc1c	A	G	1: 21,439,281 (GRCm39)	N89S	probably benign	Het
Lcor	A	G	19: 41,572,013 (GRCm39)	D256G	possibly damaging	Het
Lrrc72	T	A	12: 36,258,661 (GRCm39)		probably null	Het
Lyst	T	G	13: 13,808,719 (GRCm39)	S130A	probably benign	Het
Mast1	G	A	8: 85,642,895 (GRCm39)	R967C	probably damaging	Het
Mfng	T	C	15: 78,657,286 (GRCm39)	T63A	probably damaging	Het
Mre11a	G	A	9: 14,710,923 (GRCm39)	D206N	probably benign	Het
Myh10	A	G	11: 68,662,694 (GRCm39)		probably benign	Het
Myt1	A	G	2: 181,439,549 (GRCm39)	D357G	probably damaging	Het
Nacad	T	A	11: 6,552,540 (GRCm39)	H217L	probably benign	Het
Ncoa1	A	G	12: 4,345,433 (GRCm39)	V638A	probably damaging	Het
Nlrp3	T	G	11: 59,439,862 (GRCm39)	F480V	probably damaging	Het
Nos1ap	A	G	1: 170,146,127 (GRCm39)	W476R	possibly damaging	Het
Nr1h4	T	A	10: 89,316,421 (GRCm39)	T220S	possibly damaging	Het
Ntf5	G	T	7: 45,065,176 (GRCm39)	V103L	probably damaging	Het
Ntm	C	A	9: 29,090,393 (GRCm39)	D109Y	probably damaging	Het
Or7e178	C	T	9: 20,226,142 (GRCm39)	E17K	probably benign	Het
P2rx7	G	A	5: 122,819,015 (GRCm39)	C479Y	probably damaging	Het
Pappa2	T	A	1: 158,631,073 (GRCm39)		probably null	Het
Pikfyve	G	A	1: 65,231,454 (GRCm39)		probably null	Het
Plekhg3	T	C	12: 76,622,991 (GRCm39)	S744P	probably benign	Het
Pramel6	A	G	2: 87,339,526 (GRCm39)	R97G	probably damaging	Het
Pramel6	G	T	2: 87,339,527 (GRCm39)	R97M	probably damaging	Het
Psme4	T	C	11: 30,760,922 (GRCm39)	V397A	probably damaging	Het
Ptk2b	T	C	14: 66,396,119 (GRCm39)	D783G	probably damaging	Het
Ptma-ps1	T	A	7: 23,763,306 (GRCm39)	L17*	probably null	Het
Ralgapa2	C	A	2: 146,229,621 (GRCm39)	R1053L	probably damaging	Het
Sap130	C	T	18: 31,813,620 (GRCm39)	P559L	possibly damaging	Het
Sap30	T	C	8: 57,940,345 (GRCm39)	S86G	probably damaging	Het
Sdk2	C	T	11: 113,729,472 (GRCm39)		silent	Het
Sema3f	G	T	9: 107,561,575 (GRCm39)	Q500K	probably damaging	Het
Serpinb3d	T	C	1: 107,007,014 (GRCm39)	I231M	possibly damaging	Het
Sf3a1	T	A	11: 4,126,678 (GRCm39)	N563K	probably benign	Het
Sipa1l3	A	G	7: 29,038,592 (GRCm39)	S352P	possibly damaging	Het
Slc6a12	G	T	6: 121,324,402 (GRCm39)	E9*	probably null	Het
Srebf1	T	C	11: 60,095,319 (GRCm39)	D400G	probably damaging	Het
Swsap1	T	C	9: 21,867,988 (GRCm39)	Y87H	probably damaging	Het
Tanc2	G	A	11: 105,813,689 (GRCm39)	G1711D	possibly damaging	Het
Tas2r107	T	C	6: 131,636,951 (GRCm39)	M33V	probably benign	Het
Tdrd9	T	A	12: 112,030,061 (GRCm39)		probably benign	Het
Tdrp	T	C	8: 14,004,079 (GRCm39)	D86G	probably damaging	Het
Tmem92	A	T	11: 94,669,501 (GRCm39)	M106K	probably benign	Het
Tmf1	A	T	6: 97,138,440 (GRCm39)	C764S	possibly damaging	Het
Ttc21a	G	T	9: 119,795,823 (GRCm39)	R1219L	possibly damaging	Het
Ttn	C	T	2: 76,593,792 (GRCm39)	G18870D	probably damaging	Het
Tubgcp6	T	C	15: 88,984,811 (GRCm39)	Y1732C	probably damaging	Het
Vmn1r28	A	G	6: 58,242,912 (GRCm39)	T252A	probably benign	Het
Xirp2	A	G	2: 67,346,700 (GRCm39)	I2980M	probably damaging	Het
Zc2hc1c	A	G	12: 85,337,288 (GRCm39)	D315G	probably benign	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
R1817:Pgap1	UTSW	1	54,575,128 (GRCm39)	missense	probably benign	0.15
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'- TCATACCACAGCTACCTGGC -3'
(R):5'- ACCTTAATGTCTTTTGGGAGCATAG -3'

Sequencing Primer
(F):5'- GGAAGACGGTCATTTTTCAAATAGG -3'
(R):5'- TGGGAGCATAGTACTCGCTAATC -3'

Posted On

2014-07-14