Mutagenetix > Incidental Mutation

Incidental Mutation 'R7229:Pafah1b1'

562373

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

MMRRC Submission

045301-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7229 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

74564775-74615210 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 74573104 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 320 (I320T)

Ref Sequence

ENSEMBL: ENSMUSP00000021091 (fasta)

Gene Model

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

AlphaFold

P63005

PDB Structure

N-TERMINAL DOMAIN OF LISSENCEPHALY-1 PROTEIN (LIS-1) [X-RAY DIFFRACTION]
PAF-AH HOLOENZYME: LIS1/ALFA2 [X-RAY DIFFRACTION]

Predicted Effect

probably damaging
Transcript: ENSMUST00000021091
AA Change: I320T

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000021091
Gene: ENSMUSG00000020745
AA Change: I320T

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: I320T

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000099578
Gene: ENSMUSG00000020745
AA Change: I320T

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

100% (73/73)

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: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4931414P19Rik	T	C	14: 54,832,809 (GRCm39)	E122G	probably benign	Het
Adamts2	T	C	11: 50,682,647 (GRCm39)	Y880H	probably damaging	Het
Atp13a4	A	G	16: 29,239,723 (GRCm39)	S830P	probably benign	Het
Atp1a3	T	A	7: 24,687,410 (GRCm39)	Q696L	probably benign	Het
Brox	G	A	1: 183,073,523 (GRCm39)	R85*	probably null	Het
C130073F10Rik	T	C	4: 101,747,439 (GRCm39)	I197V	probably benign	Het
Cand2	G	A	6: 115,768,153 (GRCm39)	V433M	probably damaging	Het
Cep83	A	G	10: 94,555,527 (GRCm39)	K74E	probably damaging	Het
Chrng	A	T	1: 87,137,166 (GRCm39)	T275S	probably benign	Het
Clca3a2	T	C	3: 144,789,869 (GRCm39)	D489G	probably damaging	Het
Cmtr1	A	G	17: 29,914,398 (GRCm39)		probably null	Het
Cnga1	T	C	5: 72,775,592 (GRCm39)	N43S	probably benign	Het
Cog8	A	T	8: 107,782,984 (GRCm39)	C102S	probably damaging	Het
Cpsf3	G	A	12: 21,346,738 (GRCm39)		probably null	Het
Cyp26b1	G	A	6: 84,554,132 (GRCm39)	Q162*	probably null	Het
Elmod3	A	G	6: 72,571,736 (GRCm39)	F14S	probably benign	Het
Eps8	A	G	6: 137,516,354 (GRCm39)	S9P	probably benign	Het
Fam184b	T	C	5: 45,741,517 (GRCm39)	Q238R	probably damaging	Het
Fbxw7	T	C	3: 84,884,676 (GRCm39)	L654S	unknown	Het
Foxp1	A	T	6: 98,912,373 (GRCm39)	L580Q	unknown	Het
Galr1	A	G	18: 82,423,789 (GRCm39)	S163P	probably damaging	Het
Ganc	T	C	2: 120,258,256 (GRCm39)	F201L	possibly damaging	Het
Gin1	T	C	1: 97,712,876 (GRCm39)	F310L	probably benign	Het
Grik2	A	T	10: 48,977,512 (GRCm39)		probably null	Het
Haus1	A	T	18: 77,851,834 (GRCm39)	F94I	probably benign	Het
Hcn4	A	G	9: 58,760,682 (GRCm39)	Y409C	unknown	Het
Hspa1l	A	G	17: 35,196,231 (GRCm39)	K90R	probably benign	Het
Icam5	T	C	9: 20,948,297 (GRCm39)	S702P	possibly damaging	Het
Ifnar1	A	G	16: 91,296,444 (GRCm39)	H315R	probably benign	Het
Klra9	T	C	6: 130,168,224 (GRCm39)	H14R	probably damaging	Het
Krt78	A	G	15: 101,855,829 (GRCm39)	Y661H	probably benign	Het
Krtap11-1	T	C	16: 89,367,813 (GRCm39)	T69A	possibly damaging	Het
L3mbtl3	C	A	10: 26,168,560 (GRCm39)	S598I	unknown	Het
Lama1	A	T	17: 68,059,441 (GRCm39)	D608V		Het
Lrrc55	G	A	2: 85,026,784 (GRCm39)	T80I	probably damaging	Het
Lyst	A	T	13: 13,818,094 (GRCm39)	T1255S	probably benign	Het
Magi2	T	C	5: 20,670,586 (GRCm39)	V310A	probably damaging	Het
Med23	C	A	10: 24,777,902 (GRCm39)	A750D	probably benign	Het
Mmp2	G	A	8: 93,558,414 (GRCm39)	R161Q	probably damaging	Het
Myo15a	A	T	11: 60,387,321 (GRCm39)	I733F	probably benign	Het
Ncan	A	T	8: 70,552,961 (GRCm39)	F1090L	possibly damaging	Het
Or2ag2b	T	G	7: 106,418,202 (GRCm39)	V304G	probably damaging	Het
Otulinl	G	A	15: 27,658,273 (GRCm39)	T199M	probably benign	Het
Pcdhb1	T	A	18: 37,399,740 (GRCm39)	Y564N	probably damaging	Het
Pear1	A	G	3: 87,657,596 (GRCm39)	S988P	probably benign	Het
Pgam2	A	C	11: 5,753,013 (GRCm39)	V194G	probably damaging	Het
Plvap	A	T	8: 71,964,221 (GRCm39)	I47N	probably damaging	Het
Prdx6	A	T	1: 161,074,867 (GRCm39)	L71H	probably damaging	Het
Psmb11	G	A	14: 54,863,408 (GRCm39)	V209M	probably damaging	Het
Ptprn2	G	A	12: 117,190,845 (GRCm39)		probably null	Het
Rcn2	T	A	9: 55,964,763 (GRCm39)	N240K	probably benign	Het
Rsad2	A	T	12: 26,504,122 (GRCm39)	Y136N	probably damaging	Het
Slc12a4	T	G	8: 106,673,369 (GRCm39)	Q734P	probably benign	Het
Smarcc2	T	A	10: 128,323,917 (GRCm39)	M1085K	unknown	Het
Smg1	A	T	7: 117,776,178 (GRCm39)	C1371S	probably benign	Het
Spg11	A	T	2: 121,938,585 (GRCm39)	F456L	probably damaging	Het
Srsf10	C	T	4: 135,583,528 (GRCm39)		probably benign	Het
Stxbp5	T	C	10: 9,673,931 (GRCm39)	Y4C	probably damaging	Het
Tdrd12	T	A	7: 35,179,705 (GRCm39)	D881V	unknown	Het
Tmem171	T	C	13: 98,829,133 (GRCm39)	T6A	probably benign	Het
Tmem220	T	C	11: 66,916,989 (GRCm39)	L55P	unknown	Het
Ttn	G	T	2: 76,677,125 (GRCm39)	P11037Q	unknown	Het
Tulp4	C	T	17: 6,282,055 (GRCm39)	H695Y	probably damaging	Het
Usp47	T	C	7: 111,692,084 (GRCm39)	S849P	probably benign	Het
Vcan	G	A	13: 89,853,389 (GRCm39)	P524S	possibly damaging	Het
Vmn1r18	A	G	6: 57,367,083 (GRCm39)	M157T	probably benign	Het
Vmn2r109	A	T	17: 20,761,225 (GRCm39)	C711S	possibly damaging	Het
Wasf3	C	T	5: 146,392,463 (GRCm39)	R178C	probably damaging	Het
Wdr76	G	A	2: 121,359,401 (GRCm39)	V231I	probably damaging	Het
Xirp2	A	T	2: 67,355,895 (GRCm39)	N3552I	probably damaging	Het
Zfp804a	A	G	2: 82,088,969 (GRCm39)	T933A	probably benign	Het
Zmynd8	A	G	2: 165,699,973 (GRCm39)		probably null	Het
Zranb3	A	T	1: 127,968,630 (GRCm39)	I95K	probably benign	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
R3276: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
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'- GCTTTCTCCTCCAGAGTAGC -3'
(R):5'- TTCTTTCTAGGCTAGGTACAGCTATC -3'

Sequencing Primer
(F):5'- CCAGCACTGACTGGTTTTTATAG -3'
(R):5'- GCAAGATTTCAAGTAAATGTCA -3'

Posted On

2019-06-26