Mutagenetix > Incidental Mutation

Incidental Mutation 'R3276:Pafah1b1'

258229

Institutional Source

Beutler Lab

Gene Symbol

Pafah1b1

Ensembl Gene

ENSMUSG00000020745

Gene Name

platelet-activating factor acetylhydrolase, isoform 1b, subunit 1

Synonyms

lissencephaly-1 protein, PAF-AH 45, Pafaha, Mdsh, Lis1, LIS-1

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R3276 (G1)

Quality Score

191

Status

Validated

Chromosome

Chromosomal Location

74564775-74615210 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 74581058 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Phenylalanine at position 57 (S57F)

Ref Sequence

ENSEMBL: ENSMUSP00000118231 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021091] [ENSMUST00000102520] [ENSMUST00000155493]

AlphaFold

P63005

Predicted Effect

probably damaging
Transcript: ENSMUST00000021091
AA Change: S57F

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

SMART Domains

Protein: ENSMUSP00000021091
Gene: ENSMUSG00000020745
AA Change: S57F

Domain	Start	End	E-Value	Type
LisH	7	39	6.12e-7	SMART
WD40	97	136	2.1e-7	SMART
WD40	139	178	9.73e-12	SMART
WD40	181	220	1.1e-10	SMART
WD40	223	262	9.3e-9	SMART
WD40	265	324	4.65e-9	SMART
WD40	327	366	4.11e-10	SMART
WD40	369	408	8.81e-10	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000102520
AA Change: S57F

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

SMART Domains

Protein: ENSMUSP00000099578
Gene: ENSMUSG00000020745
AA Change: S57F

Domain	Start	End	E-Value	Type
LisH	7	39	6.12e-7	SMART
WD40	97	136	2.1e-7	SMART
WD40	139	178	9.73e-12	SMART
WD40	181	220	1.1e-10	SMART
WD40	223	262	9.3e-9	SMART
WD40	265	324	4.65e-9	SMART
WD40	327	366	4.11e-10	SMART
WD40	369	408	8.81e-10	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126341

Predicted Effect

probably damaging
Transcript: ENSMUST00000155493
AA Change: S57F

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

SMART Domains

Protein: ENSMUSP00000118231
Gene: ENSMUSG00000020745
AA Change: S57F

Domain	Start	End	E-Value	Type
LisH	7	39	6.12e-7	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156794

Meta Mutation Damage Score

0.6039

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.9%
20x: 93.7%

Validation Efficiency

96% (47/49)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This locus was identified as encoding a gene that when mutated or lost caused the lissencephaly associated with Miller-Dieker lissencephaly syndrome. This gene encodes the non-catalytic alpha subunit of the intracellular Ib isoform of platelet-activating factor acteylhydrolase, a heterotrimeric enzyme that specifically catalyzes the removal of the acetyl group at the SN-2 position of platelet-activating factor (identified as 1-O-alkyl-2-acetyl-sn-glyceryl-3-phosphorylcholine). Two other isoforms of intracellular platelet-activating factor acetylhydrolase exist: one composed of multiple subunits, the other, a single subunit. In addition, a single-subunit isoform of this enzyme is found in serum. [provided by RefSeq, Apr 2009]
PHENOTYPE: Mutations at this locus result in neuronal migration defects. Homozygous null mutants die around implantation. Different allelic combinations show variable cortical, hippocampal and olfactory disorganization and impaired spatial learning and coordination. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 62 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc12	C	T	8: 87,233,495 (GRCm39)	R1269H	probably damaging	Het
Ace	A	G	11: 105,867,528 (GRCm39)	E164G	probably null	Het
Als2	A	T	1: 59,209,167 (GRCm39)	V1464E	possibly damaging	Het
Atox1	A	G	11: 55,341,379 (GRCm39)	L52P	possibly damaging	Het
Btnl10	A	G	11: 58,813,216 (GRCm39)	K282E	probably benign	Het
Cdkn3	T	C	14: 47,008,934 (GRCm39)		probably benign	Het
Col16a1	A	G	4: 129,951,792 (GRCm39)	K72E	probably damaging	Het
Col6a5	G	A	9: 105,788,306 (GRCm39)	R1565*	probably null	Het
Col6a6	T	C	9: 105,663,429 (GRCm39)	H36R	probably benign	Het
Cyp4b1	T	C	4: 115,483,047 (GRCm39)	N415D	possibly damaging	Het
Dennd4a	G	T	9: 64,796,275 (GRCm39)	R767L	probably damaging	Het
Dhcr24	T	C	4: 106,418,436 (GRCm39)	F25L	probably benign	Het
Dhrs3	A	G	4: 144,650,510 (GRCm39)	T219A	probably benign	Het
Dhx58	A	G	11: 100,587,805 (GRCm39)	F584S	probably damaging	Het
Dmbt1	A	G	7: 130,689,801 (GRCm39)	T715A	probably benign	Het
Eogt	T	A	6: 97,108,355 (GRCm39)	I229F	probably benign	Het
Ern2	T	C	7: 121,780,187 (GRCm39)	T164A	possibly damaging	Het
Fam133b	A	T	5: 3,608,522 (GRCm39)	N84I	probably damaging	Het
Fbxl21	T	A	13: 56,684,935 (GRCm39)	Y346*	probably null	Het
Fcgbp	C	A	7: 27,791,086 (GRCm39)	H782Q	probably damaging	Het
Gm5592	A	G	7: 40,937,804 (GRCm39)	E362G	probably benign	Het
Golga3	T	C	5: 110,349,864 (GRCm39)		probably benign	Het
Gpatch2l	A	G	12: 86,291,089 (GRCm39)	T91A	possibly damaging	Het
Hsp90aa1	T	A	12: 110,662,114 (GRCm39)	M1L	possibly damaging	Het
Hsp90aa1	C	A	12: 110,662,115 (GRCm39)		probably null	Het
Itgad	C	A	7: 127,790,153 (GRCm39)	H651N	possibly damaging	Het
Itgav	A	G	2: 83,606,886 (GRCm39)	D409G	probably damaging	Het
Kcnt2	A	G	1: 140,537,377 (GRCm39)	N1119S	probably benign	Het
Klhl32	T	C	4: 24,682,063 (GRCm39)	I207V	probably benign	Het
Klk14	G	A	7: 43,341,501 (GRCm39)	C51Y	probably damaging	Het
Lhfpl5	T	C	17: 28,798,920 (GRCm39)	I143T	possibly damaging	Het
Lrrk1	T	C	7: 65,955,269 (GRCm39)	K431E	possibly damaging	Het
Mag	C	T	7: 30,601,073 (GRCm39)		probably null	Het
Maml3	A	T	3: 51,764,351 (GRCm39)	N204K	possibly damaging	Het
Mmut	A	G	17: 41,269,763 (GRCm39)		probably null	Het
Mrpl19	T	C	6: 81,941,047 (GRCm39)	S115G	probably damaging	Het
Mthfd1l	G	C	10: 4,098,025 (GRCm39)	G954A	probably damaging	Het
Myo19	A	G	11: 84,783,001 (GRCm39)	I172V	probably benign	Het
Naca	T	C	10: 127,876,530 (GRCm39)		probably benign	Het
Nfatc2	T	C	2: 168,348,914 (GRCm39)	N638D	possibly damaging	Het
Nsun6	A	G	2: 15,014,215 (GRCm39)		probably benign	Het
Or52r1c	C	A	7: 102,734,957 (GRCm39)	D72E	probably damaging	Het
Or8b49	T	A	9: 38,505,939 (GRCm39)	C141S	probably damaging	Het
Or9s27	A	G	1: 92,516,535 (GRCm39)	N161S	probably benign	Het
Padi6	A	G	4: 140,462,700 (GRCm39)	L307P	probably damaging	Het
Prcd	A	G	11: 116,550,637 (GRCm39)	E103G	possibly damaging	Het
Prkx	A	T	X: 76,814,881 (GRCm39)	F260I	probably damaging	Het
Rad54l2	A	G	9: 106,631,142 (GRCm39)		probably null	Het
Ranbp1	T	C	16: 18,065,293 (GRCm39)		probably benign	Het
Rb1cc1	T	A	1: 6,319,590 (GRCm39)	M1003K	probably benign	Het
Scap	A	T	9: 110,203,093 (GRCm39)	M256L	probably benign	Het
Sema4c	C	T	1: 36,588,960 (GRCm39)	R722H	possibly damaging	Het
Septin4	T	C	11: 87,458,070 (GRCm39)	V148A	possibly damaging	Het
Sgk1	C	T	10: 21,872,500 (GRCm39)	R171W	probably damaging	Het
Spata7	A	G	12: 98,603,857 (GRCm39)	N75D	possibly damaging	Het
Tmem120b	T	A	5: 123,252,167 (GRCm39)	I146N	probably damaging	Het
Ttc23l	A	G	15: 10,547,318 (GRCm39)	F99L	possibly damaging	Het
Ube3a	T	A	7: 58,926,267 (GRCm39)	C348*	probably null	Het
Ubr4	T	A	4: 139,149,166 (GRCm39)	D1777E	probably benign	Het
Unc79	C	A	12: 103,079,476 (GRCm39)	D1880E	probably damaging	Het
Usp36	C	T	11: 118,167,585 (GRCm39)		probably null	Het
Zswim9	T	C	7: 13,011,196 (GRCm39)	T51A	possibly damaging	Het

Other mutations in Pafah1b1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01295:Pafah1b1	APN	11	74,574,473 (GRCm39)	missense	probably damaging	1.00
IGL01861:Pafah1b1	APN	11	74,581,403 (GRCm39)	missense	possibly damaging	0.81
IGL02082:Pafah1b1	APN	11	74,590,159 (GRCm39)	missense	probably benign	0.33
IGL03180:Pafah1b1	APN	11	74,574,344 (GRCm39)	missense	possibly damaging	0.80
hotspur	UTSW	11	74,573,098 (GRCm39)	missense	probably benign	0.02
picador	UTSW	11	74,568,557 (GRCm39)	missense	probably benign
R0362:Pafah1b1	UTSW	11	74,574,457 (GRCm39)	missense	probably benign	0.01
R0462:Pafah1b1	UTSW	11	74,568,541 (GRCm39)	missense	probably benign	0.00
R1962:Pafah1b1	UTSW	11	74,590,177 (GRCm39)	start gained	probably benign
R3176:Pafah1b1	UTSW	11	74,581,058 (GRCm39)	missense	probably damaging	1.00
R3615:Pafah1b1	UTSW	11	74,581,058 (GRCm39)	missense	probably damaging	1.00
R3616:Pafah1b1	UTSW	11	74,581,058 (GRCm39)	missense	probably damaging	1.00
R4326:Pafah1b1	UTSW	11	74,573,066 (GRCm39)	missense	probably benign	0.04
R4327:Pafah1b1	UTSW	11	74,573,066 (GRCm39)	missense	probably benign	0.04
R4328:Pafah1b1	UTSW	11	74,573,066 (GRCm39)	missense	probably benign	0.04
R4776:Pafah1b1	UTSW	11	74,576,697 (GRCm39)	unclassified	probably benign
R4985:Pafah1b1	UTSW	11	74,576,814 (GRCm39)	missense	probably damaging	1.00
R5128:Pafah1b1	UTSW	11	74,570,262 (GRCm39)	intron	probably benign
R5148:Pafah1b1	UTSW	11	74,575,278 (GRCm39)	missense	probably damaging	0.99
R6406:Pafah1b1	UTSW	11	74,573,098 (GRCm39)	missense	probably benign	0.02
R6437:Pafah1b1	UTSW	11	74,568,557 (GRCm39)	missense	probably benign
R7229:Pafah1b1	UTSW	11	74,573,104 (GRCm39)	missense	probably damaging	0.99
R7480:Pafah1b1	UTSW	11	74,576,740 (GRCm39)	missense	probably damaging	1.00
R8115:Pafah1b1	UTSW	11	74,575,319 (GRCm39)	missense	probably damaging	1.00
R9042:Pafah1b1	UTSW	11	74,574,493 (GRCm39)	missense	probably benign	0.27
X0064:Pafah1b1	UTSW	11	74,580,009 (GRCm39)	missense	possibly damaging	0.62
Z1176:Pafah1b1	UTSW	11	74,581,067 (GRCm39)	missense	probably damaging	1.00
Z1176:Pafah1b1	UTSW	11	74,579,945 (GRCm39)	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- GGCAGTATAACCTATGTGCACC -3'
(R):5'- GTAGTTAGGTCAATTCAGCTATTCG -3'

Sequencing Primer
(F):5'- TAACCTATGTGCACCAATAATGAAC -3'
(R):5'- GATGTCATGGTTAAGCCAT -3'

Posted On

2015-01-23