Incidental Mutation 'R7338:Tubgcp4'
| ID |
569629 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Tubgcp4
|
| Ensembl Gene |
ENSMUSG00000027263 |
| Gene Name |
tubulin, gamma complex component 4 |
| Synonyms |
4932441P04Rik, D2Ertd435e |
| MMRRC Submission |
045428-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R7338 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
121001135-121029251 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 121024465 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Valine
at position 548
(I548V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000044049
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000039541]
[ENSMUST00000110647]
[ENSMUST00000110648]
[ENSMUST00000110657]
[ENSMUST00000110658]
[ENSMUST00000186659]
|
| AlphaFold |
Q9D4F8 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000039541
AA Change: I548V
PolyPhen 2
Score 0.018 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000044049
Gene: ENSMUSG00000027263
AA Change: I548V
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Spc97_Spc98
|
4 |
573 |
2.8e-111 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000110647
|
| SMART Domains |
Protein: ENSMUSP00000106277
Gene: ENSMUSG00000043909
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
136 |
149 |
N/A |
INTRINSIC |
|
low complexity region
|
158 |
169 |
N/A |
INTRINSIC |
|
low complexity region
|
647 |
661 |
N/A |
INTRINSIC |
|
low complexity region
|
1031 |
1042 |
N/A |
INTRINSIC |
|
low complexity region
|
1099 |
1112 |
N/A |
INTRINSIC |
|
low complexity region
|
1260 |
1272 |
N/A |
INTRINSIC |
|
low complexity region
|
1290 |
1332 |
N/A |
INTRINSIC |
|
Pfam:53-BP1_Tudor
|
1430 |
1551 |
2.5e-80 |
PFAM |
|
low complexity region
|
1581 |
1601 |
N/A |
INTRINSIC |
|
BRCT
|
1673 |
1785 |
7.13e-1 |
SMART |
|
BRCT
|
1813 |
1901 |
1.03e-6 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000110648
|
| SMART Domains |
Protein: ENSMUSP00000106278
Gene: ENSMUSG00000043909
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
136 |
149 |
N/A |
INTRINSIC |
|
low complexity region
|
158 |
169 |
N/A |
INTRINSIC |
|
low complexity region
|
647 |
661 |
N/A |
INTRINSIC |
|
low complexity region
|
1031 |
1042 |
N/A |
INTRINSIC |
|
low complexity region
|
1099 |
1112 |
N/A |
INTRINSIC |
|
low complexity region
|
1260 |
1272 |
N/A |
INTRINSIC |
|
low complexity region
|
1290 |
1332 |
N/A |
INTRINSIC |
|
low complexity region
|
1389 |
1409 |
N/A |
INTRINSIC |
|
Pfam:53-BP1_Tudor
|
1480 |
1601 |
1.5e-80 |
PFAM |
|
low complexity region
|
1631 |
1651 |
N/A |
INTRINSIC |
|
BRCT
|
1723 |
1835 |
7.13e-1 |
SMART |
|
BRCT
|
1863 |
1951 |
1.03e-6 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000110657
AA Change: I547V
PolyPhen 2
Score 0.017 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000106285
Gene: ENSMUSG00000027263
AA Change: I547V
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Spc97_Spc98
|
4 |
572 |
3.1e-115 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000110658
AA Change: I547V
PolyPhen 2
Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000106286
Gene: ENSMUSG00000027263
AA Change: I547V
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Spc97_Spc98
|
4 |
572 |
4.1e-115 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000147540
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000186659
AA Change: I547V
PolyPhen 2
Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000140417
Gene: ENSMUSG00000027263
AA Change: I547V
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Spc97_Spc98
|
4 |
572 |
4.1e-115 |
PFAM |
|
| Meta Mutation Damage Score |
0.1013 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.1%
|
| Validation Efficiency |
98% (54/55) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a component of the gamma-tubulin ring complex, which is required for microtubule nucleation. In mammalian cells, the protein localizes to centrosomes in association with gamma-tubulin. Crystal structure analysis revealed a structure composed of five helical bundles arranged around conserved hydrophobic cores. An exposed surface area located in the C-terminal domain is essential and sufficient for direct binding to gamma-tubulin. Mutations in this gene that alter microtubule organization are associated with microcephaly and chorioretinopathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2015]
|
| Allele List at MGI |
All alleles(2) : Gene trapped(2) |
| Other mutations in this stock |
Total: 56 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca3 |
T |
C |
17: 24,595,717 (GRCm39) |
S357P |
possibly damaging |
Het |
| Arhgap28 |
T |
C |
17: 68,203,106 (GRCm39) |
R166G |
probably damaging |
Het |
| Bcan |
T |
A |
3: 87,901,550 (GRCm39) |
E384V |
probably damaging |
Het |
| Bcl9l |
A |
G |
9: 44,420,005 (GRCm39) |
N1137S |
probably benign |
Het |
| Caprin1 |
A |
G |
2: 103,609,768 (GRCm39) |
L170S |
probably benign |
Het |
| Card6 |
C |
T |
15: 5,129,354 (GRCm39) |
E681K |
probably benign |
Het |
| Catsperb |
G |
A |
12: 101,447,243 (GRCm39) |
V248I |
probably benign |
Het |
| Ccnj |
T |
A |
19: 40,825,477 (GRCm39) |
H62Q |
probably damaging |
Het |
| Cd180 |
A |
C |
13: 102,842,936 (GRCm39) |
I661L |
probably benign |
Het |
| Cdk11b |
A |
G |
4: 155,732,008 (GRCm39) |
R473G |
unknown |
Het |
| Cep126 |
T |
C |
9: 8,099,799 (GRCm39) |
T912A |
possibly damaging |
Het |
| Chek2 |
T |
A |
5: 111,021,380 (GRCm39) |
V530E |
probably benign |
Het |
| Chga |
G |
T |
12: 102,529,100 (GRCm39) |
S359I |
probably damaging |
Het |
| Cnrip1 |
T |
C |
11: 17,004,657 (GRCm39) |
V69A |
probably damaging |
Het |
| Cyp2a5 |
A |
T |
7: 26,542,372 (GRCm39) |
Q458L |
probably damaging |
Het |
| Cyp2j11 |
T |
A |
4: 96,195,524 (GRCm39) |
T391S |
possibly damaging |
Het |
| Dhx16 |
T |
C |
17: 36,199,036 (GRCm39) |
L794P |
probably damaging |
Het |
| Dscaml1 |
A |
G |
9: 45,585,802 (GRCm39) |
T580A |
probably benign |
Het |
| Elmo1 |
A |
T |
13: 20,464,982 (GRCm39) |
I184L |
probably benign |
Het |
| Gabra1 |
C |
T |
11: 42,073,121 (GRCm39) |
G51S |
unknown |
Het |
| Gabrr3 |
C |
A |
16: 59,268,439 (GRCm39) |
L351I |
possibly damaging |
Het |
| Gbp7 |
A |
T |
3: 142,243,786 (GRCm39) |
N111I |
probably damaging |
Het |
| Gjd2 |
C |
T |
2: 113,841,583 (GRCm39) |
R298H |
probably damaging |
Het |
| Gm5930 |
T |
C |
14: 44,573,914 (GRCm39) |
Y141C |
probably damaging |
Het |
| Grin3a |
G |
T |
4: 49,771,238 (GRCm39) |
N511K |
probably benign |
Het |
| Hdac7 |
T |
C |
15: 97,707,903 (GRCm39) |
D122G |
probably benign |
Het |
| Ifi204 |
G |
A |
1: 173,587,703 (GRCm39) |
T152I |
possibly damaging |
Het |
| Lrrc9 |
C |
T |
12: 72,510,305 (GRCm39) |
|
probably null |
Het |
| Med21 |
T |
A |
6: 146,544,082 (GRCm39) |
|
probably benign |
Het |
| Mmp19 |
A |
T |
10: 128,634,952 (GRCm39) |
T523S |
probably benign |
Het |
| Nav3 |
G |
A |
10: 109,605,073 (GRCm39) |
T1000I |
probably benign |
Het |
| Nherf2 |
T |
A |
17: 24,869,182 (GRCm39) |
|
probably benign |
Het |
| Nin |
T |
C |
12: 70,090,838 (GRCm39) |
D859G |
|
Het |
| Nip7 |
T |
G |
8: 107,783,916 (GRCm39) |
L52R |
possibly damaging |
Het |
| Or10d1c |
A |
G |
9: 38,893,816 (GRCm39) |
Y175H |
probably damaging |
Het |
| Or5al5 |
A |
T |
2: 85,961,726 (GRCm39) |
F94I |
probably damaging |
Het |
| Or6b13 |
A |
T |
7: 139,782,446 (GRCm39) |
V79E |
probably benign |
Het |
| Otop1 |
T |
A |
5: 38,457,547 (GRCm39) |
Y435* |
probably null |
Het |
| Pak4 |
A |
G |
7: 28,264,381 (GRCm39) |
S174P |
probably benign |
Het |
| Pcsk7 |
G |
A |
9: 45,837,287 (GRCm39) |
R537Q |
probably benign |
Het |
| Podxl |
G |
A |
6: 31,505,941 (GRCm39) |
S34F |
unknown |
Het |
| Prr36 |
G |
A |
8: 4,266,212 (GRCm39) |
R113C |
probably damaging |
Het |
| Ptk7 |
T |
C |
17: 46,890,525 (GRCm39) |
I436V |
probably benign |
Het |
| Slc13a5 |
C |
T |
11: 72,157,310 (GRCm39) |
V28I |
probably benign |
Het |
| Slco6d1 |
A |
T |
1: 98,349,097 (GRCm39) |
D56V |
probably benign |
Het |
| Spg11 |
G |
A |
2: 121,885,858 (GRCm39) |
R2317W |
probably damaging |
Het |
| Stom |
T |
A |
2: 35,213,760 (GRCm39) |
|
probably null |
Het |
| Svs5 |
T |
C |
2: 164,174,728 (GRCm39) |
L8P |
possibly damaging |
Het |
| Tmem141 |
C |
A |
2: 25,511,626 (GRCm39) |
V39F |
probably damaging |
Het |
| Tmprss6 |
A |
G |
15: 78,344,019 (GRCm39) |
L181P |
probably damaging |
Het |
| Tnni3 |
A |
G |
7: 4,524,379 (GRCm39) |
S40P |
probably benign |
Het |
| Twf2 |
A |
G |
9: 106,081,138 (GRCm39) |
|
probably benign |
Het |
| Wnt5b |
C |
A |
6: 119,425,092 (GRCm39) |
|
probably null |
Het |
| Wrap73 |
A |
G |
4: 154,237,043 (GRCm39) |
D210G |
probably benign |
Het |
| Yipf4 |
T |
G |
17: 74,796,771 (GRCm39) |
S21A |
probably benign |
Het |
| Zscan20 |
A |
G |
4: 128,481,943 (GRCm39) |
M573T |
probably benign |
Het |
|
| Other mutations in Tubgcp4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00573:Tubgcp4
|
APN |
2 |
121,009,182 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL01112:Tubgcp4
|
APN |
2 |
121,004,082 (GRCm39) |
missense |
probably benign |
0.10 |
|
IGL01149:Tubgcp4
|
APN |
2 |
121,015,264 (GRCm39) |
missense |
probably null |
0.01 |
|
IGL01869:Tubgcp4
|
APN |
2 |
121,006,269 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
IGL01873:Tubgcp4
|
APN |
2 |
121,018,665 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL01888:Tubgcp4
|
APN |
2 |
121,015,228 (GRCm39) |
missense |
probably benign |
0.15 |
|
IGL03060:Tubgcp4
|
APN |
2 |
121,007,071 (GRCm39) |
splice site |
probably benign |
|
|
IGL03333:Tubgcp4
|
APN |
2 |
121,026,654 (GRCm39) |
splice site |
probably null |
|
|
FR4589:Tubgcp4
|
UTSW |
2 |
121,005,944 (GRCm39) |
critical splice donor site |
probably benign |
|
|
G5030:Tubgcp4
|
UTSW |
2 |
121,014,815 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0482:Tubgcp4
|
UTSW |
2 |
121,005,855 (GRCm39) |
missense |
probably benign |
0.02 |
|
R0512:Tubgcp4
|
UTSW |
2 |
121,005,900 (GRCm39) |
missense |
probably benign |
0.06 |
|
R1433:Tubgcp4
|
UTSW |
2 |
121,005,905 (GRCm39) |
nonsense |
probably null |
|
|
R1488:Tubgcp4
|
UTSW |
2 |
121,007,031 (GRCm39) |
missense |
possibly damaging |
0.50 |
|
R1699:Tubgcp4
|
UTSW |
2 |
121,020,374 (GRCm39) |
nonsense |
probably null |
|
|
R1760:Tubgcp4
|
UTSW |
2 |
121,019,952 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1935:Tubgcp4
|
UTSW |
2 |
121,009,147 (GRCm39) |
splice site |
probably benign |
|
|
R2249:Tubgcp4
|
UTSW |
2 |
121,014,110 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R4093:Tubgcp4
|
UTSW |
2 |
121,025,958 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4422:Tubgcp4
|
UTSW |
2 |
121,019,882 (GRCm39) |
nonsense |
probably null |
|
|
R4433:Tubgcp4
|
UTSW |
2 |
121,014,954 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4541:Tubgcp4
|
UTSW |
2 |
121,025,907 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4670:Tubgcp4
|
UTSW |
2 |
121,004,146 (GRCm39) |
nonsense |
probably null |
|
|
R4873:Tubgcp4
|
UTSW |
2 |
121,015,330 (GRCm39) |
intron |
probably benign |
|
|
R4877:Tubgcp4
|
UTSW |
2 |
121,020,343 (GRCm39) |
missense |
probably benign |
|
|
R5044:Tubgcp4
|
UTSW |
2 |
121,004,061 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5436:Tubgcp4
|
UTSW |
2 |
121,024,663 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5436:Tubgcp4
|
UTSW |
2 |
121,018,617 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5566:Tubgcp4
|
UTSW |
2 |
121,015,251 (GRCm39) |
missense |
possibly damaging |
0.61 |
|
R6110:Tubgcp4
|
UTSW |
2 |
121,024,589 (GRCm39) |
missense |
probably benign |
0.02 |
|
R6700:Tubgcp4
|
UTSW |
2 |
121,020,329 (GRCm39) |
missense |
probably benign |
0.11 |
|
R6980:Tubgcp4
|
UTSW |
2 |
121,025,946 (GRCm39) |
missense |
probably benign |
0.28 |
|
R6999:Tubgcp4
|
UTSW |
2 |
121,022,778 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7388:Tubgcp4
|
UTSW |
2 |
121,020,447 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7410:Tubgcp4
|
UTSW |
2 |
121,014,890 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8048:Tubgcp4
|
UTSW |
2 |
121,013,981 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8129:Tubgcp4
|
UTSW |
2 |
121,004,109 (GRCm39) |
missense |
possibly damaging |
0.80 |
|
R8414:Tubgcp4
|
UTSW |
2 |
121,024,634 (GRCm39) |
missense |
probably benign |
0.02 |
|
R9006:Tubgcp4
|
UTSW |
2 |
121,015,251 (GRCm39) |
missense |
probably benign |
0.35 |
|
R9050:Tubgcp4
|
UTSW |
2 |
121,004,079 (GRCm39) |
missense |
probably benign |
0.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TCACTGGTCAGCCTAAAGTG -3'
(R):5'- GAACATGCGATGAATAACAGTCTC -3'
Sequencing Primer
(F):5'- GACCAACCCTGAAAAGTTGTCCTTTG -3'
(R):5'- GTCTCATATCTCGTCAAGTCCAAGAG -3'
|
| Posted On |
2019-09-13 |
Incidental Mutation