Mutagenetix > Incidental Mutation

Incidental Mutation 'R7943:Pgap3'

649177

Institutional Source

Beutler Lab

Gene Symbol

Pgap3

Ensembl Gene

ENSMUSG00000038208

Gene Name

post-GPI attachment to proteins 3

Synonyms

CAB2, Perld1, D430035D22Rik

MMRRC Submission

045989-MU

Accession Numbers

Essential gene?

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

Stock #

R7943 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

98279503-98291316 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 98281227 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Glutamine at position 262 (L262Q)

Ref Sequence

ENSEMBL: ENSMUSP00000088337 (fasta)

Gene Model

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

AlphaFold

A2A559

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

probably damaging
Transcript: ENSMUST00000090827
AA Change: L262Q

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000088337
Gene: ENSMUSG00000038208
AA Change: L262Q

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000128897
AA Change: L211Q

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000119668
Gene: ENSMUSG00000038208
AA Change: L211Q

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

0.7906

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.0%

Validation Efficiency

100% (68/68)

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb1a	C	T	5: 8,736,222 (GRCm39)	T205I	probably benign	Het
Acsbg1	T	C	9: 54,530,021 (GRCm39)	H225R	probably damaging	Het
Anks1	T	A	17: 28,204,178 (GRCm39)	Y209N	probably damaging	Het
Appl1	T	A	14: 26,667,525 (GRCm39)	I377L	probably benign	Het
Arl9	A	T	5: 77,158,395 (GRCm39)	D159V	probably damaging	Het
Arsa	A	C	15: 89,358,292 (GRCm39)	L339R	probably damaging	Het
C2	A	G	17: 35,091,354 (GRCm39)	L380P	probably damaging	Het
Ccdc13	A	G	9: 121,628,196 (GRCm39)	C97R	unknown	Het
Ccdc74a	A	G	16: 17,468,416 (GRCm39)	H346R	probably benign	Het
Ccnl1	T	C	3: 65,864,326 (GRCm39)	I152V	probably benign	Het
Cd4	C	T	6: 124,847,207 (GRCm39)		probably null	Het
Ceacam5	A	T	7: 17,479,491 (GRCm39)	I203L	probably benign	Het
Ckap2	C	A	8: 22,665,090 (GRCm39)	R458L	probably damaging	Het
Cldn10	T	C	14: 119,099,271 (GRCm39)		probably null	Het
Col27a1	C	T	4: 63,236,520 (GRCm39)	R1377C	unknown	Het
Cry1	A	T	10: 84,978,984 (GRCm39)	M514K	probably benign	Het
Crybg2	T	G	4: 133,800,295 (GRCm39)	V176G	probably damaging	Het
Cyp2j5	C	T	4: 96,547,849 (GRCm39)	G131D	possibly damaging	Het
Ddx46	A	G	13: 55,817,535 (GRCm39)	Y720C	probably damaging	Het
Dock10	A	T	1: 80,626,006 (GRCm39)	V44D	probably damaging	Het
Eif1ad8	C	T	12: 87,563,773 (GRCm39)	A36V	probably damaging	Het
Enam	A	T	5: 88,636,410 (GRCm39)		probably null	Het
Fam184a	C	A	10: 53,509,802 (GRCm39)	E126*	probably null	Het
Fam184a	C	T	10: 53,523,137 (GRCm39)	A956T	probably damaging	Het
Fbxw10	A	T	11: 62,741,487 (GRCm39)	R202*	probably null	Het
Fnip1	A	G	11: 54,393,214 (GRCm39)	E550G	probably damaging	Het
Gpr149	A	G	3: 62,438,132 (GRCm39)	L675P	probably damaging	Het
Hivep3	T	C	4: 119,989,554 (GRCm39)	Y2002H	probably benign	Het
Hp	A	G	8: 110,302,187 (GRCm39)	Y254H	probably damaging	Het
Ighg1	G	T	12: 113,293,957 (GRCm39)	T62N		Het
Jcad	A	G	18: 4,672,700 (GRCm39)	E154G	probably damaging	Het
Kmt2a	A	G	9: 44,760,437 (GRCm39)	S471P	probably damaging	Het
Med13	A	G	11: 86,169,352 (GRCm39)	V1968A	probably damaging	Het
Mknk2	T	A	10: 80,511,701 (GRCm39)	Q3L	probably benign	Het
Nup98	G	A	7: 101,844,029 (GRCm39)	T65I	probably benign	Het
Or10p21	T	A	10: 128,847,934 (GRCm39)	M260K	possibly damaging	Het
Or51f1e	G	A	7: 102,747,153 (GRCm39)	M68I	probably damaging	Het
Or5m11	A	G	2: 85,782,342 (GRCm39)	T312A	probably benign	Het
Or9i14	A	T	19: 13,792,600 (GRCm39)	M118K	probably damaging	Het
Pcdhgb4	C	T	18: 37,855,063 (GRCm39)	T486I	probably benign	Het
Perm1	T	A	4: 156,302,991 (GRCm39)	F512I	probably damaging	Het
Pklr	A	C	3: 89,048,814 (GRCm39)	Y126S	probably damaging	Het
Ppl	C	T	16: 4,906,725 (GRCm39)	R1190H	probably damaging	Het
Ppm1k	T	C	6: 57,501,813 (GRCm39)	T117A	probably benign	Het
Prkd2	G	A	7: 16,584,244 (GRCm39)	E366K	probably benign	Het
Psd	C	A	19: 46,313,169 (GRCm39)	C67F	possibly damaging	Het
Ptpra	T	A	2: 30,322,056 (GRCm39)	F100L	probably damaging	Het
Rftn1	G	T	17: 50,354,408 (GRCm39)	A318D	probably damaging	Het
Rock1	T	C	18: 10,112,357 (GRCm39)	E466G	probably damaging	Het
Sec16b	A	T	1: 157,382,327 (GRCm39)	M588L	probably benign	Het
Serpina1f	T	A	12: 103,659,949 (GRCm39)	H111L	probably damaging	Het
Sf3a1	T	C	11: 4,116,537 (GRCm39)	I76T	possibly damaging	Het
Shcbp1	A	T	8: 4,798,812 (GRCm39)	L369Q	possibly damaging	Het
Spef2	A	G	15: 9,601,171 (GRCm39)	M1697T	unknown	Het
St7	G	A	6: 17,844,911 (GRCm39)	C133Y	probably damaging	Het
Tdpoz6	A	T	3: 93,600,070 (GRCm39)	C100S	probably benign	Het
Tex19.1	T	A	11: 121,037,986 (GRCm39)	W115R	possibly damaging	Het
Tfrc	T	A	16: 32,449,039 (GRCm39)	I726N	probably benign	Het
Thbs1	A	G	2: 117,950,098 (GRCm39)		probably null	Het
Trim43a	C	T	9: 88,464,238 (GRCm39)	P50S	probably benign	Het
Trpm4	A	T	7: 44,958,105 (GRCm39)	V935E	probably damaging	Het
Ttc12	A	T	9: 49,381,620 (GRCm39)	V117D	possibly damaging	Het
Ulbp1	T	C	10: 7,407,053 (GRCm39)	T82A	probably damaging	Het
Usp13	C	T	3: 32,931,089 (GRCm39)	H288Y	probably damaging	Het
Vmn2r82	A	G	10: 79,232,079 (GRCm39)	K693E	possibly damaging	Het
Vmn2r90	A	G	17: 17,932,566 (GRCm39)	T158A	probably damaging	Het
Vps8	A	G	16: 21,296,622 (GRCm39)	K540R	possibly damaging	Het
Zfp143	T	A	7: 109,671,681 (GRCm39)		probably null	Het
Zfp709	G	T	8: 72,643,933 (GRCm39)	C454F	probably damaging	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
R5493:Pgap3	UTSW	11	98,281,540 (GRCm39)	missense	possibly damaging	0.87
R5783:Pgap3	UTSW	11	98,281,290 (GRCm39)	missense	probably benign
R7722:Pgap3	UTSW	11	98,281,610 (GRCm39)	missense	probably benign	0.00
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'- GTTCTGAGAACGTCCCAGTC -3'
(R):5'- AGAGCTGTAGTTGGGCACAG -3'

Sequencing Primer
(F):5'- CAAGTGGGTATGGGGAGCCC -3'
(R):5'- GGGCACAGGGTGGATTC -3'

Posted On

2020-09-15