Incidental Mutation 'IGL02147:Pcyt1a'
| ID |
281821 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Pcyt1a
|
| Ensembl Gene |
ENSMUSG00000005615 |
| Gene Name |
phosphate cytidylyltransferase 1, choline, alpha isoform |
| Synonyms |
CTalpha, Cctalpha, Cttalpha, Ctpct, CTP:phosphocholine cytidylyltransferase alpha |
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
IGL02147
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
16 |
| Chromosomal Location |
32249739-32293883 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 32280916 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Lysine
at position 105
(N105K)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000110793
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000079791]
[ENSMUST00000104893]
[ENSMUST00000115137]
[ENSMUST00000115140]
|
| AlphaFold |
P49586 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000079791
AA Change: N105K
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000078721
Gene: ENSMUSG00000005615
AA Change: N105K
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:CTP_transf_2
|
80 |
208 |
6.4e-24 |
PFAM |
|
low complexity region
|
244 |
262 |
N/A |
INTRINSIC |
|
low complexity region
|
328 |
352 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000104893
AA Change: N105K
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000130056
Gene: ENSMUSG00000005615
AA Change: N105K
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:CTP_transf_2
|
80 |
208 |
6.4e-24 |
PFAM |
|
low complexity region
|
244 |
262 |
N/A |
INTRINSIC |
|
low complexity region
|
328 |
352 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000115137
AA Change: N105K
PolyPhen 2
Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000110790
Gene: ENSMUSG00000005615
AA Change: N105K
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:CTP_transf_2
|
80 |
201 |
4.1e-22 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000115140
AA Change: N105K
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000110793
Gene: ENSMUSG00000005615
AA Change: N105K
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:CTP_transf_like
|
80 |
208 |
3.2e-33 |
PFAM |
|
low complexity region
|
244 |
262 |
N/A |
INTRINSIC |
|
low complexity region
|
328 |
352 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000231920
|
| Coding Region Coverage |
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the cytidylyltransferase family and is involved in the regulation of phosphatidylcholine biosynthesis. Mutations in this gene are associated with spondylometaphyseal dysplasia with cone-rod dystrophy. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2015]
PHENOTYPE: Embryos homozygous for a targeted null mutation fail to form blastocysts, do not develop past E3.5, and fail to implant. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 36 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700021P04Rik |
T |
C |
19: 24,042,327 (GRCm39) |
|
noncoding transcript |
Het |
| Acadsb |
T |
A |
7: 131,027,610 (GRCm39) |
|
probably benign |
Het |
| Ambra1 |
A |
G |
2: 91,598,064 (GRCm39) |
H75R |
probably benign |
Het |
| Arhgef28 |
T |
A |
13: 98,097,822 (GRCm39) |
I931F |
probably damaging |
Het |
| Cdk5 |
T |
C |
5: 24,625,318 (GRCm39) |
N165D |
probably benign |
Het |
| Col4a2 |
A |
T |
8: 11,458,140 (GRCm39) |
Y272F |
probably benign |
Het |
| Csde1 |
T |
A |
3: 102,947,250 (GRCm39) |
D67E |
probably damaging |
Het |
| Dhx34 |
T |
C |
7: 15,937,928 (GRCm39) |
H724R |
probably benign |
Het |
| Dhx57 |
T |
C |
17: 80,567,752 (GRCm39) |
D777G |
possibly damaging |
Het |
| Fat3 |
A |
C |
9: 15,907,281 (GRCm39) |
V2907G |
probably damaging |
Het |
| Fst |
T |
C |
13: 114,590,896 (GRCm39) |
Y290C |
probably damaging |
Het |
| Ighg2b |
A |
T |
12: 113,270,011 (GRCm39) |
*336R |
probably null |
Het |
| Igkv4-92 |
C |
T |
6: 68,732,236 (GRCm39) |
S46N |
probably damaging |
Het |
| Kdm2b |
C |
T |
5: 123,085,898 (GRCm39) |
E238K |
probably damaging |
Het |
| Lgalsl2 |
T |
A |
7: 5,362,732 (GRCm39) |
I121N |
probably damaging |
Het |
| Lmtk2 |
A |
G |
5: 144,093,754 (GRCm39) |
M244V |
possibly damaging |
Het |
| Mcoln1 |
T |
C |
8: 3,558,379 (GRCm39) |
F211S |
probably benign |
Het |
| Mib2 |
C |
A |
4: 155,742,144 (GRCm39) |
R209L |
probably benign |
Het |
| Msx3 |
C |
A |
7: 139,628,798 (GRCm39) |
V39L |
possibly damaging |
Het |
| Mtnr1b |
A |
G |
9: 15,774,672 (GRCm39) |
F129S |
probably damaging |
Het |
| Nr3c2 |
A |
G |
8: 77,635,696 (GRCm39) |
S266G |
probably damaging |
Het |
| Nup160 |
G |
T |
2: 90,534,285 (GRCm39) |
L703F |
probably benign |
Het |
| Or10c1 |
T |
A |
17: 37,521,877 (GRCm39) |
Y289F |
probably damaging |
Het |
| Or5t5 |
A |
G |
2: 86,616,494 (GRCm39) |
N140S |
probably benign |
Het |
| Pdhx |
A |
G |
2: 102,860,686 (GRCm39) |
|
probably benign |
Het |
| Qpct |
T |
C |
17: 79,378,145 (GRCm39) |
V105A |
probably damaging |
Het |
| Ros1 |
A |
C |
10: 51,996,991 (GRCm39) |
F1227C |
probably damaging |
Het |
| Rrp12 |
A |
T |
19: 41,874,620 (GRCm39) |
V342E |
probably damaging |
Het |
| Sart3 |
A |
G |
5: 113,901,004 (GRCm39) |
|
probably benign |
Het |
| Slc6a18 |
T |
A |
13: 73,816,281 (GRCm39) |
K366M |
probably damaging |
Het |
| Smarca4 |
A |
G |
9: 21,546,999 (GRCm39) |
N175D |
probably damaging |
Het |
| Sox14 |
T |
C |
9: 99,757,598 (GRCm39) |
K47R |
probably damaging |
Het |
| Trcg1 |
A |
T |
9: 57,153,132 (GRCm39) |
I592F |
probably benign |
Het |
| Ush2a |
T |
C |
1: 188,596,900 (GRCm39) |
M3880T |
probably benign |
Het |
| Usp20 |
T |
C |
2: 30,896,413 (GRCm39) |
F172S |
probably damaging |
Het |
| Vmn2r4 |
C |
T |
3: 64,305,782 (GRCm39) |
|
probably benign |
Het |
|
| Other mutations in Pcyt1a |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00503:Pcyt1a
|
APN |
16 |
32,285,919 (GRCm39) |
missense |
probably damaging |
0.99 |
|
willingly
|
UTSW |
16 |
32,285,899 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R0164:Pcyt1a
|
UTSW |
16 |
32,289,004 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0164:Pcyt1a
|
UTSW |
16 |
32,289,004 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1529:Pcyt1a
|
UTSW |
16 |
32,270,611 (GRCm39) |
missense |
possibly damaging |
0.45 |
|
R1607:Pcyt1a
|
UTSW |
16 |
32,285,937 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R4693:Pcyt1a
|
UTSW |
16 |
32,289,042 (GRCm39) |
unclassified |
probably benign |
|
|
R4998:Pcyt1a
|
UTSW |
16 |
32,270,660 (GRCm39) |
splice site |
probably benign |
|
|
R6488:Pcyt1a
|
UTSW |
16 |
32,285,899 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R6852:Pcyt1a
|
UTSW |
16 |
32,288,938 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9091:Pcyt1a
|
UTSW |
16 |
32,285,332 (GRCm39) |
missense |
probably benign |
|
|
R9254:Pcyt1a
|
UTSW |
16 |
32,288,894 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9270:Pcyt1a
|
UTSW |
16 |
32,285,332 (GRCm39) |
missense |
probably benign |
|
|
Z1177:Pcyt1a
|
UTSW |
16 |
32,290,278 (GRCm39) |
missense |
probably benign |
|
|
| Posted On |
2015-04-16 |
Incidental Mutation