Mutagenetix > Incidental Mutation

Incidental Mutation 'R6980:Tubgcp4'

543739

Institutional Source

Beutler Lab

Gene Symbol

Tubgcp4

Ensembl Gene

ENSMUSG00000027263

Gene Name

tubulin, gamma complex component 4

Synonyms

4932441P04Rik, D2Ertd435e

MMRRC Submission

045088-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6980 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

121001135-121029251 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 121025946 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 596 (V596A)

Ref Sequence

ENSEMBL: ENSMUSP00000140417 (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: V597A

PolyPhen 2 Score 0.140 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000044049
Gene: ENSMUSG00000027263
AA Change: V597A

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

SMART Domains

Protein: ENSMUSP00000106285
Gene: ENSMUSG00000027263

Domain	Start	End	E-Value	Type
Pfam:Spc97_Spc98	4	572	3.1e-115	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000110658
AA Change: V596A

PolyPhen 2 Score 0.284 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000106286
Gene: ENSMUSG00000027263
AA Change: V596A

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: V596A

PolyPhen 2 Score 0.284 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000140417
Gene: ENSMUSG00000027263
AA Change: V596A

Domain	Start	End	E-Value	Type
Pfam:Spc97_Spc98	4	572	4.1e-115	PFAM

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.2%

Validation Efficiency

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: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca2	C	A	2: 25,330,878 (GRCm39)	R1189S	possibly damaging	Het
Abcf2	T	C	5: 24,770,970 (GRCm39)	Q594R	probably benign	Het
Abhd18	G	A	3: 40,888,215 (GRCm39)	S353N	probably benign	Het
Adrb1	G	T	19: 56,712,046 (GRCm39)	A415S	probably benign	Het
Art2b	T	C	7: 101,229,680 (GRCm39)	N73S	probably benign	Het
BC028528	CTCACTGGTTCTGTGGTCACTGGTTCTGTGGTCACTGGTTCTGTGGTCACTGGTT	CTCACTGGTTCTGTGGTCACTGGTTCTGTGGTCACTGGTTCTGTGGTCACTGGTTCTGTGGTCACTGGTT	3: 95,795,448 (GRCm39)		probably benign	Het
BC028528	CACTGGTTCTGTGGT	CACTGGTTCTGTGGTTACTGGTTCTGTGGT	3: 95,795,480 (GRCm39)		probably benign	Het
BC028528	ACTGGTTCTGTGGTCACTGGTTCTGTGGTCACTGGTTCTGTGGTC	ACTGGTTCTGTGGTCTCTGGTTCTGTGGTCACTGGTTCTGTGGTCACTGGTTCTGTGGTC	3: 95,795,451 (GRCm39)		probably benign	Het
Cacna1a	A	G	8: 85,338,914 (GRCm39)	M1753V	possibly damaging	Het
Cbx8	A	T	11: 118,930,287 (GRCm39)	I102N	possibly damaging	Het
Ccdc178	T	A	18: 22,238,620 (GRCm39)	E332D	probably benign	Het
Cdhr17	T	A	5: 17,031,944 (GRCm39)	V533D	possibly damaging	Het
Cfap74	G	A	4: 155,550,809 (GRCm39)		probably benign	Het
Chat	A	T	14: 32,146,111 (GRCm39)	M354K	probably benign	Het
Cmas	A	G	6: 142,702,526 (GRCm39)	T10A	probably damaging	Het
Cyb561d1	A	T	3: 108,107,475 (GRCm39)	L51H	probably benign	Het
D030056L22Rik	A	T	19: 18,694,629 (GRCm39)	N128I	probably damaging	Het
D130043K22Rik	G	T	13: 25,048,764 (GRCm39)	A423S	probably damaging	Het
Dnah14	T	C	1: 181,475,795 (GRCm39)	I1349T	probably benign	Het
Dnajb3	T	G	1: 88,132,736 (GRCm39)	D222A	probably damaging	Het
Dtx1	T	C	5: 120,819,422 (GRCm39)	E592G	probably damaging	Het
Dzank1	C	T	2: 144,332,056 (GRCm39)	G427R	possibly damaging	Het
E130308A19Rik	A	C	4: 59,719,991 (GRCm39)	K508Q	probably damaging	Het
Eif4e1b	T	A	13: 54,931,916 (GRCm39)		probably null	Het
Ell2	A	G	13: 75,904,495 (GRCm39)	M159V	probably null	Het
Eml4	G	A	17: 83,758,446 (GRCm39)	V377I	probably benign	Het
Fryl	A	T	5: 73,207,773 (GRCm39)	S2466T	probably benign	Het
Gfpt1	C	A	6: 87,054,071 (GRCm39)	T426K	probably damaging	Het
Gm49355	T	C	14: 12,307,173 (GRCm38)		probably benign	Het
Gm5114	T	C	7: 39,058,624 (GRCm39)	I332V	probably benign	Het
Gpr15	T	A	16: 58,539,105 (GRCm39)		probably benign	Het
Gpr179	T	C	11: 97,225,684 (GRCm39)	E2157G	probably benign	Het
Gramd4	A	G	15: 86,016,170 (GRCm39)	N482S	probably benign	Het
Hfm1	A	T	5: 107,028,343 (GRCm39)	I829K	probably benign	Het
Hydin	A	T	8: 111,139,916 (GRCm39)	E728D	possibly damaging	Het
Ifngr2	T	A	16: 91,356,895 (GRCm39)	V143E	probably damaging	Het
Ift172	T	C	5: 31,414,730 (GRCm39)	D1390G	probably benign	Het
Kdf1	A	T	4: 133,256,138 (GRCm39)	D285V	probably damaging	Het
Mast4	C	T	13: 102,941,155 (GRCm39)	V301I	probably damaging	Het
Mdn1	G	A	4: 32,726,942 (GRCm39)		probably null	Het
Megf11	A	G	9: 64,613,132 (GRCm39)	E1016G	probably damaging	Het
Mixl1	G	A	1: 180,524,453 (GRCm39)	A42V	possibly damaging	Het
Mpp2	A	G	11: 101,950,154 (GRCm39)	W567R	probably damaging	Het
Mrgpra6	A	G	7: 46,838,697 (GRCm39)	L136P	probably damaging	Het
Mroh7	T	A	4: 106,557,434 (GRCm39)	I759L	probably benign	Het
Nrxn2	A	G	19: 6,500,609 (GRCm39)	D277G	probably benign	Het
Nup210l	A	T	3: 90,027,234 (GRCm39)	K205N	probably benign	Het
Or4g17	A	G	2: 111,209,620 (GRCm39)	I92V	possibly damaging	Het
Or4p4b-ps1	A	G	2: 88,453,939 (GRCm39)	*97W	probably null	Het
Or52e19b	T	C	7: 103,032,303 (GRCm39)	E302G	probably benign	Het
Or5al6	A	T	2: 85,976,681 (GRCm39)	Y132*	probably null	Het
Oxnad1	C	T	14: 31,807,576 (GRCm39)		probably benign	Het
Pamr1	C	T	2: 102,472,549 (GRCm39)	T616I	probably benign	Het
Pcdhgb5	C	T	18: 37,866,592 (GRCm39)	H796Y	possibly damaging	Het
Pdlim7	G	T	13: 55,656,041 (GRCm39)	D126E	probably benign	Het
Pfdn2	C	T	1: 171,185,465 (GRCm39)		probably benign	Het
Piezo2	T	A	18: 63,216,032 (GRCm39)		probably null	Het
Pms2	A	T	5: 143,848,842 (GRCm39)	I43L	probably benign	Het
Prex2	T	A	1: 11,232,487 (GRCm39)	S851R	probably benign	Het
Ptpn4	T	A	1: 119,671,151 (GRCm39)	E202D	possibly damaging	Het
Rnf40	T	A	7: 127,193,849 (GRCm39)	V455E	probably damaging	Het
Rp1l1	A	G	14: 64,266,169 (GRCm39)	N585S	probably benign	Het
Rrp12	A	G	19: 41,878,582 (GRCm39)	S188P	probably damaging	Het
Rsbn1l	T	A	5: 21,101,482 (GRCm39)	H686L	probably benign	Het
Runx2	C	T	17: 45,046,203 (GRCm39)	V107I	possibly damaging	Het
Rusc2	A	G	4: 43,422,846 (GRCm39)	I994M	probably benign	Het
Ryr1	T	A	7: 28,808,812 (GRCm39)	D420V	probably benign	Het
Sash1	T	C	10: 8,605,612 (GRCm39)	Q926R	probably benign	Het
Scgb3a2	T	A	18: 43,897,499 (GRCm39)	I6N	probably damaging	Het
Sdc3	T	A	4: 130,544,233 (GRCm39)		probably benign	Het
Sik2	A	G	9: 50,808,755 (GRCm39)	V658A	probably benign	Het
Slc25a39	A	G	11: 102,296,601 (GRCm39)	V81A	probably damaging	Het
Snai2	T	A	16: 14,526,113 (GRCm39)	S255T	possibly damaging	Het
Sorbs1	A	T	19: 40,316,060 (GRCm39)	Y371*	probably null	Het
Spata31d1b	A	T	13: 59,863,236 (GRCm39)	H128L	probably benign	Het
Spdl1	A	T	11: 34,721,706 (GRCm39)	M1K	probably null	Het
Tgm3	T	A	2: 129,868,697 (GRCm39)	N211K	probably benign	Het
Tmem116	T	C	5: 121,606,050 (GRCm39)		probably null	Het
Tmem132e	T	A	11: 82,329,212 (GRCm39)		probably null	Het
Tmem53	T	C	4: 117,125,705 (GRCm39)	C251R	probably damaging	Het
Trcg1	A	C	9: 57,152,856 (GRCm39)	D551A	probably damaging	Het
Trp63	T	A	16: 25,620,843 (GRCm39)	F12I	probably benign	Het
Ttn	C	T	2: 76,709,401 (GRCm39)		probably null	Het
Ugt2a3	A	C	5: 87,473,491 (GRCm39)	H475Q	probably damaging	Het
Unc79	G	A	12: 103,025,759 (GRCm39)	R382K	probably damaging	Het
Vmn2r58	T	C	7: 41,513,662 (GRCm39)	H327R	possibly damaging	Het
Vmn2r7	G	A	3: 64,623,987 (GRCm39)	T111I	possibly damaging	Het
Zfp318	T	A	17: 46,708,138 (GRCm39)	Y399N	probably damaging	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
R6999:Tubgcp4	UTSW	2	121,022,778 (GRCm39)	missense	probably damaging	1.00
R7338:Tubgcp4	UTSW	2	121,024,465 (GRCm39)	missense	probably benign	0.02
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'- GTTACTTGGGAGGGCCAAACAG -3'
(R):5'- ACCGATACCAGCGCTTTTATC -3'

Sequencing Primer
(F):5'- CCAAACAGCTTTGAAGGTTGC -3'
(R):5'- GATACCAGCGCTTTTATCTTTTTATC -3'

Posted On

2019-05-13