Mutagenetix > Incidental Mutation

Incidental Mutation 'R0512:Tubgcp4'

47872

Institutional Source

Beutler Lab

Gene Symbol

Tubgcp4

Ensembl Gene

ENSMUSG00000027263

Gene Name

tubulin, gamma complex component 4

Synonyms

4932441P04Rik, D2Ertd435e

MMRRC Submission

038706-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0512 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

121001135-121029251 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 121005900 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 96 (V96A)

Ref Sequence

ENSEMBL: ENSMUSP00000106285 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000039541] [ENSMUST00000110657] [ENSMUST00000110658] [ENSMUST00000186659] [ENSMUST00000163766] [ENSMUST00000146243]

AlphaFold

Q9D4F8

Predicted Effect

probably benign
Transcript: ENSMUST00000039541
AA Change: V96A

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000044049
Gene: ENSMUSG00000027263
AA Change: V96A

Domain	Start	End	E-Value	Type
Pfam:Spc97_Spc98	4	573	2.8e-111	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000110657
AA Change: V96A

PolyPhen 2 Score 0.065 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000106285
Gene: ENSMUSG00000027263
AA Change: V96A

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

Predicted Effect

probably benign
Transcript: ENSMUST00000110658
AA Change: V96A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000106286
Gene: ENSMUSG00000027263
AA Change: V96A

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130929

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000133773

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000135555

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138601

Predicted Effect

probably benign
Transcript: ENSMUST00000186659
AA Change: V96A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000140417
Gene: ENSMUSG00000027263
AA Change: V96A

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144076

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144123

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154633

Predicted Effect

probably benign
Transcript: ENSMUST00000163766

SMART Domains

Protein: ENSMUSP00000125987
Gene: ENSMUSG00000050619

Domain	Start	End	E-Value	Type
SCAN	13	125	5.83e-70	SMART
Pfam:Myb_DNA-bind_4	238	323	5.9e-21	PFAM
Pfam:Myb_DNA-bind_4	434	519	1.3e-21	PFAM
low complexity region	553	567	N/A	INTRINSIC
ZnF_C2H2	700	722	2.99e-4	SMART
ZnF_C2H2	728	750	2.75e-3	SMART
ZnF_C2H2	756	778	8.02e-5	SMART
ZnF_C2H2	784	806	1.13e-4	SMART
ZnF_C2H2	812	834	1.18e-2	SMART
ZnF_C2H2	840	862	1.33e-1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000146243

SMART Domains

Protein: ENSMUSP00000120997
Gene: ENSMUSG00000050619

Domain	Start	End	E-Value	Type
SCAN	13	118	4.23e-58	SMART

Meta Mutation Damage Score

0.0606

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.7%
20x: 93.8%

Validation Efficiency

100% (92/92)

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: 91 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930519G04Rik	T	G	5: 115,001,569 (GRCm39)	M22R	probably benign	Het
Abca8b	C	A	11: 109,841,476 (GRCm39)	M1039I	probably benign	Het
Actn2	A	T	13: 12,292,301 (GRCm39)	I653N	probably damaging	Het
Actr8	G	T	14: 29,700,513 (GRCm39)	V31L	probably benign	Het
Adam30	T	C	3: 98,069,441 (GRCm39)	C425R	probably damaging	Het
Armc1	A	G	3: 19,203,659 (GRCm39)	V89A	possibly damaging	Het
Atr	T	C	9: 95,817,579 (GRCm39)	M2090T	probably damaging	Het
Braf	T	A	6: 39,641,923 (GRCm39)		probably benign	Het
Cant1	A	T	11: 118,302,091 (GRCm39)	N75K	probably benign	Het
Chd7	C	T	4: 8,805,139 (GRCm39)		probably benign	Het
Clec16a	A	G	16: 10,432,444 (GRCm39)	Y488C	probably damaging	Het
Col6a3	A	T	1: 90,749,520 (GRCm39)		probably benign	Het
Col9a2	T	A	4: 120,911,504 (GRCm39)	M615K	probably benign	Het
Dedd	G	A	1: 171,168,498 (GRCm39)	R228H	probably damaging	Het
Dhtkd1	C	T	2: 5,908,902 (GRCm39)	D731N	probably damaging	Het
Ercc2	A	G	7: 19,127,812 (GRCm39)	T651A	probably damaging	Het
Fam13a	T	A	6: 58,933,684 (GRCm39)	D302V	probably damaging	Het
Fam193a	T	C	5: 34,583,735 (GRCm39)	S19P	probably damaging	Het
Fam43a	T	C	16: 30,420,553 (GRCm39)	V379A	possibly damaging	Het
Fat1	C	A	8: 45,404,369 (GRCm39)	Y373*	probably null	Het
Fbxl15	A	C	19: 46,317,861 (GRCm39)	D181A	probably damaging	Het
Flt3	A	T	5: 147,278,080 (GRCm39)	C831*	probably null	Het
Foxj3	T	A	4: 119,443,033 (GRCm39)		probably benign	Het
Glul	T	C	1: 153,781,132 (GRCm39)		probably benign	Het
Gm16380	A	T	9: 53,791,529 (GRCm39)		noncoding transcript	Het
Gm7964	A	T	7: 83,405,158 (GRCm39)		noncoding transcript	Het
Hipk1	A	G	3: 103,667,890 (GRCm39)	F559S	possibly damaging	Het
Hnf4g	A	T	3: 3,716,682 (GRCm39)	I284F	probably damaging	Het
Hoxa13	CCG	CCGCG	6: 52,237,618 (GRCm39)		probably null	Het
Icosl	A	G	10: 77,907,800 (GRCm39)	N120S	possibly damaging	Het
Ift172	A	G	5: 31,442,821 (GRCm39)	V155A	possibly damaging	Het
Kdm4c	A	G	4: 74,252,031 (GRCm39)	E426G	probably benign	Het
Kif23	A	G	9: 61,826,257 (GRCm39)		probably benign	Het
Krt81	C	A	15: 101,361,508 (GRCm39)	R24L	possibly damaging	Het
Lama1	G	A	17: 68,086,129 (GRCm39)	C1456Y	possibly damaging	Het
Lamc3	T	A	2: 31,827,980 (GRCm39)	L1378Q	probably damaging	Het
Larp1b	T	A	3: 40,924,469 (GRCm39)	L121M	probably benign	Het
Lepr	T	A	4: 101,649,216 (GRCm39)	D872E	probably damaging	Het
Lepr	A	C	4: 101,671,901 (GRCm39)	D975A	possibly damaging	Het
Magi1	A	G	6: 93,671,045 (GRCm39)	V1068A	probably damaging	Het
Malt1	T	A	18: 65,591,271 (GRCm39)	N358K	probably damaging	Het
Mfap4	T	A	11: 61,378,771 (GRCm39)	W240R	probably damaging	Het
Mis18a	A	G	16: 90,523,244 (GRCm39)	V84A	possibly damaging	Het
Mns1	A	G	9: 72,356,753 (GRCm39)	E308G	possibly damaging	Het
Mpp2	C	A	11: 101,953,116 (GRCm39)	L258F	possibly damaging	Het
Myh2	A	G	11: 67,079,504 (GRCm39)	E987G	probably damaging	Het
Myof	A	G	19: 37,942,972 (GRCm39)	V702A	possibly damaging	Het
Nhs	C	A	X: 160,620,355 (GRCm39)	R1467I	probably damaging	Het
Nrxn2	A	G	19: 6,567,228 (GRCm39)	T1360A	probably damaging	Het
Obox6	A	G	7: 15,567,874 (GRCm39)	I191T	probably benign	Het
Pacs2	G	T	12: 113,014,547 (GRCm39)	R236L	probably damaging	Het
Pcdhb2	T	G	18: 37,429,032 (GRCm39)	V335G	probably damaging	Het
Phyhipl	T	C	10: 70,404,748 (GRCm39)	I140M	probably damaging	Het
Pkhd1	T	C	1: 20,380,738 (GRCm39)		probably benign	Het
Ppp1r3b	T	G	8: 35,851,571 (GRCm39)	C137G	probably damaging	Het
Prdm13	T	A	4: 21,678,490 (GRCm39)	I667F	probably damaging	Het
Prex2	A	G	1: 11,270,157 (GRCm39)	M1281V	probably benign	Het
Rab40b	A	G	11: 121,250,412 (GRCm39)	F81L	probably damaging	Het
Rb1cc1	T	C	1: 6,318,767 (GRCm39)	S729P	probably damaging	Het
Rcl1	A	G	19: 29,105,497 (GRCm39)	D228G	probably damaging	Het
Rhbdf1	A	T	11: 32,160,875 (GRCm39)	C19*	probably null	Het
Rif1	GCCACCA	GCCA	2: 52,000,336 (GRCm39)		probably benign	Het
Rnf150	G	A	8: 83,590,807 (GRCm39)	V57M	probably benign	Het
Rp9	A	G	9: 22,370,015 (GRCm39)	F51L	probably benign	Het
Sav1	A	T	12: 70,015,975 (GRCm39)	Y274*	probably null	Het
Scn4a	A	T	11: 106,236,503 (GRCm39)	D252E	probably damaging	Het
Scn5a	T	C	9: 119,379,724 (GRCm39)	T187A	probably damaging	Het
Sigirr	T	A	7: 140,672,333 (GRCm39)	D229V	probably benign	Het
Slc39a13	T	C	2: 90,896,031 (GRCm39)	S157G	possibly damaging	Het
Slc6a20a	A	G	9: 123,489,471 (GRCm39)	S191P	probably damaging	Het
Sorl1	C	A	9: 41,979,128 (GRCm39)	A457S	probably benign	Het
Spag5	A	G	11: 78,210,412 (GRCm39)		probably benign	Het
Spon1	A	G	7: 113,436,066 (GRCm39)	E119G	possibly damaging	Het
Spred2	T	A	11: 19,958,485 (GRCm39)		probably benign	Het
Sprr3	T	G	3: 92,364,784 (GRCm39)	Q20P	possibly damaging	Het
Strn3	A	T	12: 51,673,966 (GRCm39)	F464L	possibly damaging	Het
Sun1	A	G	5: 139,220,602 (GRCm39)		probably benign	Het
Sypl2	A	G	3: 108,133,486 (GRCm39)	W28R	possibly damaging	Het
Syt5	A	T	7: 4,545,813 (GRCm39)	V150D	probably damaging	Het
Tasor	T	C	14: 27,168,363 (GRCm39)	F302L	probably damaging	Het
Thsd7a	A	G	6: 12,379,604 (GRCm39)	I940T	possibly damaging	Het
Tlcd3b	C	T	7: 126,426,795 (GRCm39)	R73C	probably damaging	Het
Tnrc6a	T	A	7: 122,785,951 (GRCm39)		probably benign	Het
Trp53	T	A	11: 69,479,509 (GRCm39)	L203Q	probably damaging	Het
Usp17la	A	G	7: 104,510,246 (GRCm39)	T284A	possibly damaging	Het
Usp34	T	C	11: 23,401,997 (GRCm39)	M2409T	probably benign	Het
Vmn2r100	C	A	17: 19,742,382 (GRCm39)	P252Q	possibly damaging	Het
Vmn2r56	A	G	7: 12,449,350 (GRCm39)	I296T	probably benign	Het
Vmn2r67	A	G	7: 84,799,900 (GRCm39)	V446A	probably damaging	Het
Zfp217	C	T	2: 169,957,382 (GRCm39)	A539T	probably benign	Het
Zfp267	T	C	3: 36,220,262 (GRCm39)	C762R	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
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
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'- GTCAGCACTTCTTTCCTGAGGCAC -3'
(R):5'- TTTGAAAACCGTACCCTCTAGCCAC -3'

Sequencing Primer
(F):5'- CCTGAGGCACCTTGCATAC -3'
(R):5'- CACGGGAAATAGCTCACTCTTAC -3'

Posted On

2013-06-12