Incidental Mutation 'R4327:Pafah1b1'
| ID |
324429 |
| 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 |
041097-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R4327 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
74564775-74615210 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 74573066 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 333
(T333A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000099578
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000021091]
[ENSMUST00000102520]
|
| AlphaFold |
P63005 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000021091
AA Change: T333A
PolyPhen 2
Score 0.043 (Sensitivity: 0.94; Specificity: 0.83)
|
| SMART Domains |
Protein: ENSMUSP00000021091
Gene: ENSMUSG00000020745
AA Change: T333A
| 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 benign
Transcript: ENSMUST00000102520
AA Change: T333A
PolyPhen 2
Score 0.043 (Sensitivity: 0.94; Specificity: 0.83)
|
| SMART Domains |
Protein: ENSMUSP00000099578
Gene: ENSMUSG00000020745
AA Change: T333A
| 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 |
noncoding transcript
Transcript: ENSMUST00000156794
|
| Meta Mutation Damage Score |
0.1265 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.8%
- 10x: 97.6%
- 20x: 95.9%
|
| Validation Efficiency |
98% (64/65) |
| 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: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700019A02Rik |
T |
C |
1: 53,221,664 (GRCm39) |
D55G |
possibly damaging |
Het |
| Alcam |
T |
C |
16: 52,073,579 (GRCm39) |
N549S |
possibly damaging |
Het |
| Arap2 |
A |
T |
5: 62,779,206 (GRCm39) |
H1461Q |
possibly damaging |
Het |
| Arhgef12 |
C |
A |
9: 42,886,525 (GRCm39) |
E1152* |
probably null |
Het |
| Arrdc5 |
T |
C |
17: 56,601,420 (GRCm39) |
E235G |
possibly damaging |
Het |
| Atp1a3 |
A |
G |
7: 24,687,056 (GRCm39) |
|
probably benign |
Het |
| Bcl2l1 |
A |
G |
2: 152,624,099 (GRCm39) |
V223A |
probably benign |
Het |
| C9orf72 |
T |
A |
4: 35,225,985 (GRCm39) |
|
probably benign |
Het |
| Cela3b |
G |
T |
4: 137,151,242 (GRCm39) |
A137E |
probably benign |
Het |
| Col13a1 |
T |
C |
10: 61,699,758 (GRCm39) |
T476A |
unknown |
Het |
| Col16a1 |
T |
C |
4: 129,988,344 (GRCm39) |
|
probably null |
Het |
| Ctcfl |
G |
A |
2: 172,955,299 (GRCm39) |
|
probably benign |
Het |
| Cyp2j8 |
T |
A |
4: 96,395,566 (GRCm39) |
T20S |
probably benign |
Het |
| Fastkd2 |
A |
G |
1: 63,791,516 (GRCm39) |
K675E |
probably benign |
Het |
| Fsip2 |
A |
T |
2: 82,817,403 (GRCm39) |
I4379F |
probably benign |
Het |
| Gm10722 |
T |
C |
9: 3,000,937 (GRCm39) |
C6R |
probably benign |
Het |
| Hmgxb3 |
A |
T |
18: 61,300,611 (GRCm39) |
M155K |
probably benign |
Het |
| Ip6k2 |
G |
A |
9: 108,682,847 (GRCm39) |
R319Q |
probably benign |
Het |
| Kcnn1 |
A |
T |
8: 71,305,307 (GRCm39) |
V301E |
probably damaging |
Het |
| Kcnq4 |
T |
C |
4: 120,568,561 (GRCm39) |
E385G |
probably benign |
Het |
| Klhl28 |
G |
A |
12: 64,996,952 (GRCm39) |
A463V |
probably damaging |
Het |
| Lhb |
A |
G |
7: 45,070,383 (GRCm39) |
R3G |
possibly damaging |
Het |
| Lingo2 |
T |
A |
4: 35,708,462 (GRCm39) |
D506V |
probably damaging |
Het |
| Macf1 |
C |
T |
4: 123,276,005 (GRCm39) |
A4176T |
probably damaging |
Het |
| Marchf6 |
C |
T |
15: 31,498,887 (GRCm39) |
E137K |
probably benign |
Het |
| Med12l |
T |
C |
3: 59,172,688 (GRCm39) |
S1813P |
probably benign |
Het |
| Mpp3 |
T |
C |
11: 101,914,337 (GRCm39) |
|
probably benign |
Het |
| Muc2 |
A |
C |
7: 141,281,577 (GRCm39) |
S479R |
probably damaging |
Het |
| Or11g27 |
T |
A |
14: 50,770,971 (GRCm39) |
I34N |
probably benign |
Het |
| Or12e10 |
G |
T |
2: 87,640,496 (GRCm39) |
V111L |
probably benign |
Het |
| Or2t1 |
T |
A |
14: 14,328,193 (GRCm38) |
F27L |
probably damaging |
Het |
| Or52n1 |
G |
A |
7: 104,382,833 (GRCm39) |
T246I |
probably damaging |
Het |
| Palm |
G |
A |
10: 79,643,520 (GRCm39) |
G83S |
probably benign |
Het |
| Pcdhb9 |
A |
T |
18: 37,534,875 (GRCm39) |
S290C |
probably benign |
Het |
| Pcdhb9 |
G |
T |
18: 37,534,876 (GRCm39) |
S290I |
probably benign |
Het |
| Pdgfrb |
A |
T |
18: 61,204,792 (GRCm39) |
I551F |
possibly damaging |
Het |
| Pex26 |
A |
T |
6: 121,164,373 (GRCm39) |
E172V |
probably damaging |
Het |
| Pitrm1 |
A |
G |
13: 6,629,809 (GRCm39) |
|
probably benign |
Het |
| Ptprs |
C |
A |
17: 56,754,468 (GRCm39) |
A191S |
possibly damaging |
Het |
| Rdm1 |
T |
A |
11: 101,521,734 (GRCm39) |
V92E |
probably damaging |
Het |
| Scn7a |
A |
G |
2: 66,567,815 (GRCm39) |
F260L |
probably damaging |
Het |
| Serpinb3a |
T |
A |
1: 106,979,500 (GRCm39) |
M1L |
probably damaging |
Het |
| Sh3d19 |
T |
C |
3: 86,031,020 (GRCm39) |
I728T |
probably benign |
Het |
| Sin3a |
T |
C |
9: 57,002,642 (GRCm39) |
L178P |
probably damaging |
Het |
| Slc13a1 |
A |
G |
6: 24,103,478 (GRCm39) |
V355A |
probably benign |
Het |
| St7 |
G |
A |
6: 17,819,287 (GRCm39) |
V64M |
probably damaging |
Het |
| Tcf25 |
T |
A |
8: 124,127,882 (GRCm39) |
L622* |
probably null |
Het |
| Tiam1 |
A |
G |
16: 89,652,779 (GRCm39) |
V781A |
possibly damaging |
Het |
| Tigd2 |
C |
A |
6: 59,187,562 (GRCm39) |
T143K |
probably benign |
Het |
| Tmem107 |
G |
T |
11: 68,962,301 (GRCm39) |
|
probably null |
Het |
| Tmem161b |
G |
A |
13: 84,399,359 (GRCm39) |
G5D |
probably damaging |
Het |
| Tonsl |
G |
A |
15: 76,523,916 (GRCm39) |
A28V |
probably benign |
Het |
| Treml4 |
T |
C |
17: 48,581,417 (GRCm39) |
Y222H |
probably damaging |
Het |
| Trp53bp1 |
A |
T |
2: 121,087,131 (GRCm39) |
V175D |
probably damaging |
Het |
| Zfp184 |
T |
C |
13: 22,144,072 (GRCm39) |
Y593H |
probably damaging |
Het |
| Zfp286 |
A |
G |
11: 62,670,844 (GRCm39) |
C410R |
probably damaging |
Het |
| Zfp934 |
T |
G |
13: 62,665,373 (GRCm39) |
N312H |
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 |
|
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'- GAGCTTTCTCCTCCAGAGTAGC -3'
(R):5'- TTTCTTTCTAGGCTAGGTACAGC -3'
Sequencing Primer
(F):5'- CCAGCACTGACTGGTTTTTATAG -3'
(R):5'- GCTAGGTACAGCTATCTATATATTTC -3'
|
| Posted On |
2015-06-24 |
Incidental Mutation