Mutagenetix > Incidental Mutation

Incidental Mutation 'R5493:Pgap3'

432192

Institutional Source

Beutler Lab

Gene Symbol

Pgap3

Ensembl Gene

ENSMUSG00000038208

Gene Name

post-GPI attachment to proteins 3

Synonyms

CAB2, Perld1, D430035D22Rik

MMRRC Submission

043054-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.391) question?

Stock #

R5493 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

98279503-98291316 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to C at 98281540 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 168 (F168L)

Ref Sequence

ENSEMBL: ENSMUSP00000119668 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000041301] [ENSMUST00000090827] [ENSMUST00000128897]

AlphaFold

A2A559

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000041218

Predicted Effect

probably benign
Transcript: ENSMUST00000041301

SMART Domains

Protein: ENSMUSP00000035549
Gene: ENSMUSG00000038216

Domain	Start	End	E-Value	Type
Pfam:NNMT_PNMT_TEMT	25	290	1.2e-94	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000090827
AA Change: F219L

PolyPhen 2 Score 0.573 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000088337
Gene: ENSMUSG00000038208
AA Change: F219L

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
Pfam:Per1	54	306	6.3e-96	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000124527

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128058

Predicted Effect

possibly damaging
Transcript: ENSMUST00000128897
AA Change: F168L

PolyPhen 2 Score 0.873 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000119668
Gene: ENSMUSG00000038208
AA Change: F168L

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
Pfam:Per1	51	96	6.2e-14	PFAM
Pfam:Per1	93	256	7.3e-59	PFAM

Meta Mutation Damage Score

0.9282

Coding Region Coverage

1x: 98.3%
3x: 97.3%
10x: 95.1%
20x: 90.4%

Validation Efficiency

99% (80/81)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a glycosylphosphatidylinositol (GPI)-specific phospholipase that primarily localizes to the Golgi apparatus. This ubiquitously expressed gene is predicted to encode a seven-transmembrane protein that removes unsaturated fatty acids from the sn-2 position of GPI. The remodeling of the constituent fatty acids on GPI is thought to be important for the proper association between GPI-anchored proteins and lipid rafts. The tethering of proteins to plasma membranes via posttranslational GPI-anchoring is thought to play a role in protein sorting and trafficking. Mutations in this gene cause the autosomal recessive neurologic disorder hyperphosphatasia with mental retardation syndrome 4 (HPMRS4). Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Apr 2014]
PHENOTYPE: Mice homozygous for a targeted allele exhibit abnormal head and tail morphology, growth retardation, limb glasping, altered T cell proliferation response and increased susceptibility to EAE. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2510009E07Rik	A	G	16: 21,471,993 (GRCm39)	S236P	possibly damaging	Het
A830018L16Rik	C	T	1: 11,615,431 (GRCm39)	R135C	probably damaging	Het
Agpat3	A	G	10: 78,120,069 (GRCm39)	V155A	possibly damaging	Het
Aldh18a1	C	T	19: 40,539,734 (GRCm39)	R747Q	probably damaging	Het
Aloxe3	A	T	11: 69,019,443 (GRCm39)	R119*	probably null	Het
Asap1	A	G	15: 64,002,000 (GRCm39)	V460A	possibly damaging	Het
Bicral	C	A	17: 47,112,620 (GRCm39)	R860L	possibly damaging	Het
Cd180	T	A	13: 102,842,649 (GRCm39)	I565N	probably benign	Het
Cdk13	T	C	13: 17,978,147 (GRCm39)		probably benign	Het
Cdkn2d	T	C	9: 21,200,303 (GRCm39)	D156G	probably benign	Het
Clrn1	A	G	3: 58,753,837 (GRCm39)	S175P	probably damaging	Het
Coro7	A	G	16: 4,450,351 (GRCm39)	L535S	probably damaging	Het
Cse1l	A	G	2: 166,783,110 (GRCm39)		probably benign	Het
Cyp2a12	T	C	7: 26,728,550 (GRCm39)	L7P	unknown	Het
D130043K22Rik	A	G	13: 25,047,586 (GRCm39)	Y377C	probably damaging	Het
Dctn1	G	T	6: 83,159,546 (GRCm39)	R8L	possibly damaging	Het
Duox2	T	C	2: 122,111,977 (GRCm39)	Q1341R	probably damaging	Het
Eif2b3	A	G	4: 116,943,919 (GRCm39)	D447G	possibly damaging	Het
Eif4a3l1	C	G	6: 136,306,555 (GRCm39)	R339G	probably damaging	Het
Fbxw25	T	C	9: 109,481,984 (GRCm39)	Y234C	probably benign	Het
Gcnt2	A	G	13: 41,107,076 (GRCm39)	N315S	possibly damaging	Het
Gm20730	A	T	6: 43,058,746 (GRCm39)	V22E	possibly damaging	Het
Gm4847	T	A	1: 166,457,890 (GRCm39)	I488F	probably damaging	Het
Gmds	A	T	13: 32,124,488 (GRCm39)	M290K	probably benign	Het
Gtf3c1	T	C	7: 125,269,716 (GRCm39)	N699S	probably damaging	Het
Hk3	A	G	13: 55,158,984 (GRCm39)	V479A	probably damaging	Het
Ifnlr1	G	A	4: 135,432,877 (GRCm39)	V438M	probably benign	Het
Il12rb1	C	A	8: 71,262,483 (GRCm39)	P26T	probably benign	Het
Il4i1	G	T	7: 44,489,477 (GRCm39)	R414L	possibly damaging	Het
Ipo4	T	C	14: 55,868,327 (GRCm39)	N490S	probably benign	Het
Kcnmb2	A	G	3: 32,252,291 (GRCm39)	E164G	probably damaging	Het
Kcns1	G	A	2: 164,009,899 (GRCm39)	L287F	probably benign	Het
Kdm1a	ACC	AC	4: 136,284,732 (GRCm39)		probably null	Het
Klk14	G	A	7: 43,341,501 (GRCm39)	C51Y	probably damaging	Het
Knl1	T	A	2: 118,899,211 (GRCm39)	I304K	probably damaging	Het
Ksr2	G	T	5: 117,846,175 (GRCm39)	V681F	probably damaging	Het
Lypd2	T	C	15: 74,606,127 (GRCm39)	T4A	probably benign	Het
Man1a	A	G	10: 53,950,576 (GRCm39)	V182A	probably benign	Het
Or12j4	A	T	7: 140,046,720 (GRCm39)	D202V	probably damaging	Het
Or13e8	A	G	4: 43,696,225 (GRCm39)	F316S	possibly damaging	Het
Or2w2	A	T	13: 21,758,042 (GRCm39)	C195S	probably damaging	Het
Or51f5	A	T	7: 102,424,315 (GRCm39)	R195W	probably benign	Het
Or56b1b	T	C	7: 108,164,774 (GRCm39)	D76G	probably benign	Het
Pcdha2	C	A	18: 37,072,562 (GRCm39)	F64L	probably damaging	Het
Pip5k1b	T	C	19: 24,416,439 (GRCm39)	N16S	probably benign	Het
Ppip5k1	T	A	2: 121,167,253 (GRCm39)	H41L	probably damaging	Het
Ppp1r9a	A	G	6: 5,159,702 (GRCm39)	R1080G	probably damaging	Het
Qrich2	A	C	11: 116,336,774 (GRCm39)		probably null	Het
Rbl2	C	T	8: 91,842,447 (GRCm39)	P1034L	probably damaging	Het
Rbpjl	GCC	GC	2: 164,256,330 (GRCm39)		probably null	Het
Rin2	A	G	2: 145,702,629 (GRCm39)	S442G	probably damaging	Het
Rtca	C	T	3: 116,293,280 (GRCm39)	R71Q	probably benign	Het
Serpind1	A	T	16: 17,157,902 (GRCm39)	N366I	probably damaging	Het
Shox2	C	G	3: 66,888,796 (GRCm39)	G32R	probably damaging	Het
Sp3	T	A	2: 72,768,466 (GRCm39)	N766Y	probably damaging	Het
Spag7	T	A	11: 70,560,059 (GRCm39)	S17C	probably null	Het
Stk25	A	T	1: 93,563,031 (GRCm39)	F7I	probably benign	Het
Tbx15	G	A	3: 99,259,880 (GRCm39)	G584S	probably benign	Het
Tenm2	T	C	11: 36,755,503 (GRCm39)	D165G	probably benign	Het
Tox2	C	A	2: 163,046,649 (GRCm39)	S42*	probably null	Het
Vmn1r39	A	G	6: 66,781,754 (GRCm39)	V188A	probably damaging	Het
Zbtb5	A	T	4: 44,993,941 (GRCm39)	M481K	probably benign	Het
Zfp26	T	C	9: 20,355,615 (GRCm39)	T56A	possibly damaging	Het
Zfp459	C	A	13: 67,556,498 (GRCm39)	C195F	probably damaging	Het
Zfp703	C	T	8: 27,469,233 (GRCm39)	P299L	probably damaging	Het
Zfp764	A	G	7: 127,004,105 (GRCm39)	I342T	probably benign	Het
Zfp942	T	C	17: 22,151,985 (GRCm39)	N7D	probably null	Het

Other mutations in Pgap3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01942:Pgap3	APN	11	98,288,780 (GRCm39)	missense	probably damaging	1.00
IGL03409:Pgap3	APN	11	98,289,764 (GRCm39)	missense	possibly damaging	0.95
R0053:Pgap3	UTSW	11	98,281,924 (GRCm39)	missense	probably benign	0.16
R0053:Pgap3	UTSW	11	98,281,924 (GRCm39)	missense	probably benign	0.16
R1185:Pgap3	UTSW	11	98,281,960 (GRCm39)	missense	probably damaging	1.00
R1185:Pgap3	UTSW	11	98,281,960 (GRCm39)	missense	probably damaging	1.00
R1185:Pgap3	UTSW	11	98,281,960 (GRCm39)	missense	probably damaging	1.00
R1579:Pgap3	UTSW	11	98,280,879 (GRCm39)	missense	probably benign
R1938:Pgap3	UTSW	11	98,291,040 (GRCm39)	critical splice donor site	probably null
R2117:Pgap3	UTSW	11	98,281,933 (GRCm39)	missense	probably damaging	0.99
R2367:Pgap3	UTSW	11	98,281,985 (GRCm39)	splice site	probably null
R3854:Pgap3	UTSW	11	98,281,638 (GRCm39)	missense	possibly damaging	0.49
R4820:Pgap3	UTSW	11	98,281,300 (GRCm39)	missense	probably damaging	1.00
R5208:Pgap3	UTSW	11	98,288,874 (GRCm39)	missense	probably damaging	1.00
R5783:Pgap3	UTSW	11	98,281,290 (GRCm39)	missense	probably benign
R7722:Pgap3	UTSW	11	98,281,610 (GRCm39)	missense	probably benign	0.00
R7943:Pgap3	UTSW	11	98,281,227 (GRCm39)	missense	probably damaging	1.00
R8347:Pgap3	UTSW	11	98,281,575 (GRCm39)	small deletion	probably benign
R8878:Pgap3	UTSW	11	98,281,924 (GRCm39)	missense	probably benign	0.16
R8888:Pgap3	UTSW	11	98,281,602 (GRCm39)	missense	possibly damaging	0.73
R8895:Pgap3	UTSW	11	98,281,602 (GRCm39)	missense	possibly damaging	0.73
R9466:Pgap3	UTSW	11	98,289,796 (GRCm39)	missense	probably benign	0.01
R9531:Pgap3	UTSW	11	98,288,823 (GRCm39)	missense	probably damaging	1.00
X0026:Pgap3	UTSW	11	98,281,305 (GRCm39)	missense	possibly damaging	0.80

Predicted Primers

PCR Primer
(F):5'- ACAGGAGAGATTTACTCACTGGATC -3'
(R):5'- AGGGAGCCTTCAACCCTTTG -3'

Sequencing Primer
(F):5'- GGATCTTCCCCTGGACTCTGG -3'
(R):5'- CTTTGGGCAAGGAAATAGTTGAG -3'

Posted On

2016-10-05