Mutagenetix > Incidental Mutations

Incidental Mutation 'R5044:Tubgcp4'

394234

Institutional Source

Beutler Lab

Gene Symbol

Tubgcp4

Ensembl Gene

ENSMUSG00000027263

Gene Name

tubulin, gamma complex associated protein 4

Synonyms

D2Ertd435e, 4932441P04Rik

MMRRC Submission

042634-MU

Accession Numbers

Genbank: NM_153387

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R5044 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

121170654-121198770 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 121173580 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 34 (L34P)

Ref Sequence

ENSEMBL: ENSMUSP00000044049 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000039541] [ENSMUST00000079024] [ENSMUST00000110657] [ENSMUST00000110658] [ENSMUST00000110661] [ENSMUST00000146243] [ENSMUST00000163766] [ENSMUST00000186659]

AlphaFold

Q9D4F8

Predicted Effect

probably damaging
Transcript: ENSMUST00000039541
AA Change: L34P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000044049
Gene: ENSMUSG00000027263
AA Change: L34P

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

Predicted Effect

probably benign
Transcript: ENSMUST00000079024

SMART Domains

Protein: ENSMUSP00000078033
Gene: ENSMUSG00000050619

Domain	Start	End	E-Value	Type
SCAN	13	125	5.83e-70	SMART
Pfam:Myb_DNA-bind_4	238	323	3e-21	PFAM
Pfam:Myb_DNA-bind_4	399	484	4.1e-22	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000110657
AA Change: L34P

PolyPhen 2 Score 0.584 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000106285
Gene: ENSMUSG00000027263
AA Change: L34P

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000110658
AA Change: L34P

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000106286
Gene: ENSMUSG00000027263
AA Change: L34P

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

Predicted Effect

probably benign
Transcript: ENSMUST00000110661

SMART Domains

Protein: ENSMUSP00000106289
Gene: ENSMUSG00000050619

Domain	Start	End	E-Value	Type
SCAN	13	125	5.83e-70	SMART
Pfam:Myb_DNA-bind_4	238	323	5.4e-21	PFAM
Pfam:Myb_DNA-bind_4	399	484	7.4e-22	PFAM
low complexity region	518	532	N/A	INTRINSIC
ZnF_C2H2	665	687	2.99e-4	SMART
ZnF_C2H2	693	715	2.75e-3	SMART
ZnF_C2H2	721	743	8.02e-5	SMART
ZnF_C2H2	749	771	1.13e-4	SMART
ZnF_C2H2	777	799	1.18e-2	SMART
ZnF_C2H2	805	827	1.33e-1	SMART

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

noncoding transcript
Transcript: ENSMUST00000144076

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144123

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

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 damaging
Transcript: ENSMUST00000186659
AA Change: L34P

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000140417
Gene: ENSMUSG00000027263
AA Change: L34P

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

Meta Mutation Damage Score

0.8761

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.6%
20x: 93.3%

Validation Efficiency

96% (73/76)

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: 65 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca13	T	A	11: 9,373,323	F3387I	possibly damaging	Het
Acacb	T	A	5: 114,166,027	S170R	probably benign	Het
Adamtsl4	A	G	3: 95,681,650		probably null	Het
Adgrv1	A	G	13: 81,488,931	C3464R	probably benign	Het
Apbb1	A	T	7: 105,565,682		probably benign	Het
Cad	A	G	5: 31,055,021	T23A	probably benign	Het
Cdca7	A	G	2: 72,483,415	R183G	probably benign	Het
Cdpf1	T	C	15: 85,809,312	T5A	probably benign	Het
Cep85	T	C	4: 134,156,179	D133G	probably damaging	Het
Chrna9	T	C	5: 65,971,016	L189P	probably damaging	Het
Clca1	A	C	3: 145,007,928		probably null	Het
Cntn1	G	T	15: 92,242,995	V201F	probably damaging	Het
Col4a3	A	G	1: 82,666,546	E352G	unknown	Het
Ddhd2	T	C	8: 25,752,137	Y237C	probably damaging	Het
Dnah6	A	C	6: 73,037,622	F3609V	probably benign	Het
Epha3	T	C	16: 63,602,287	K580R	possibly damaging	Het
Fam135b	T	C	15: 71,462,711	N878S	probably benign	Het
Fam71e2	T	C	7: 4,758,661	N351D	probably benign	Het
Fbn1	T	G	2: 125,329,102	T1938P	probably damaging	Het
Foxg1	T	C	12: 49,385,186	V234A	probably damaging	Het
Glt1d1	A	T	5: 127,644,414	N55I	probably benign	Het
Gm17641	C	A	3: 68,869,474		probably benign	Het
Gm7665	A	G	18: 16,274,731		noncoding transcript	Het
Hgf	A	C	5: 16,614,894	N541T	probably benign	Het
Hipk2	G	A	6: 38,818,879	P152S	probably benign	Het
Jarid2	C	T	13: 44,906,565	L720F	probably damaging	Het
Kifc5b	A	G	17: 26,924,787	E511G	probably damaging	Het
Ldlr	G	A	9: 21,735,242	A235T	probably benign	Het
Lmln	A	G	16: 33,074,180	D231G	possibly damaging	Het
Lrp1	A	G	10: 127,567,495	C2070R	probably damaging	Het
Mbl1	A	G	14: 41,158,724	T190A	possibly damaging	Het
Mpdz	A	T	4: 81,381,697	S355T	probably benign	Het
Muc19	C	T	15: 91,888,138		noncoding transcript	Het
Mycbp2	A	C	14: 103,139,235		probably null	Het
Naa20	T	C	2: 145,915,842	S164P	probably damaging	Het
Nme4	A	T	17: 26,093,833		probably benign	Het
Npas2	A	T	1: 39,347,506	R619*	probably null	Het
Nudt19	G	A	7: 35,555,746	T20I	possibly damaging	Het
Olfr1224-ps1	T	A	2: 89,156,939	K79*	probably null	Het
Olfr1447	A	G	19: 12,901,001	Y260H	probably damaging	Het
Pitpnc1	A	G	11: 107,296,228	Y90H	possibly damaging	Het
Rcor2	A	G	19: 7,269,785	T6A	probably benign	Het
Rif1	T	A	2: 52,109,928	S1131R	probably damaging	Het
Rtkn	T	A	6: 83,150,991	D377E	probably benign	Het
Rtn4rl2	T	A	2: 84,872,502	N242I	probably damaging	Het
Sbno2	G	A	10: 80,062,188	L719F	probably benign	Het
Scn11a	G	T	9: 119,819,831	D55E	probably damaging	Het
Setd1b	T	A	5: 123,151,866	I632N	unknown	Het
Spaca6	A	G	17: 17,831,196	T45A	probably benign	Het
Srpk2	A	T	5: 23,524,392	D416E	possibly damaging	Het
Sspo	A	T	6: 48,466,955		probably null	Het
Sycp1	A	T	3: 102,845,054	I804N	probably benign	Het
Tdp2	G	A	13: 24,831,826	R32Q	probably benign	Het
Tgfbr3	A	G	5: 107,136,929	V618A	possibly damaging	Het
Tmc3	C	T	7: 83,609,118	P439S	probably benign	Het
Tnxb	A	T	17: 34,717,483	D2740V	probably damaging	Het
Tspyl4	A	G	10: 34,297,937	T142A	probably benign	Het
Ttn	T	C	2: 76,880,441		probably benign	Het
Tubgcp6	G	T	15: 89,099,545		probably benign	Het
Unc79	T	A	12: 103,112,703	V1690E	probably benign	Het
Vps4b	T	C	1: 106,796,418		probably null	Het
Wtap	A	G	17: 12,967,638	S341P	possibly damaging	Het
Wwc1	T	C	11: 35,883,345	T363A	probably benign	Het
Zbtb8a	G	A	4: 129,360,500	T67M	probably damaging	Het
Zfp865	T	C	7: 5,034,669		probably benign	Het

Other mutations in Tubgcp4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00573:Tubgcp4	APN	2	121178701	missense	probably damaging	0.99
IGL01112:Tubgcp4	APN	2	121173601	missense	probably benign	0.10
IGL01149:Tubgcp4	APN	2	121184783	missense	probably null	0.01
IGL01869:Tubgcp4	APN	2	121175788	missense	possibly damaging	0.95
IGL01873:Tubgcp4	APN	2	121188184	critical splice donor site	probably null
IGL01888:Tubgcp4	APN	2	121184747	missense	probably benign	0.15
IGL03060:Tubgcp4	APN	2	121176590	splice site	probably benign
IGL03333:Tubgcp4	APN	2	121196173	splice site	probably null
FR4589:Tubgcp4	UTSW	2	121175463	critical splice donor site	probably benign
G5030:Tubgcp4	UTSW	2	121184334	missense	probably damaging	1.00
R0482:Tubgcp4	UTSW	2	121175374	missense	probably benign	0.02
R0512:Tubgcp4	UTSW	2	121175419	missense	probably benign	0.06
R1433:Tubgcp4	UTSW	2	121175424	nonsense	probably null
R1488:Tubgcp4	UTSW	2	121176550	missense	possibly damaging	0.50
R1699:Tubgcp4	UTSW	2	121189893	nonsense	probably null
R1760:Tubgcp4	UTSW	2	121189471	critical splice donor site	probably null
R1935:Tubgcp4	UTSW	2	121178666	splice site	probably benign
R2249:Tubgcp4	UTSW	2	121183629	missense	possibly damaging	0.86
R4093:Tubgcp4	UTSW	2	121195477	missense	probably benign	0.01
R4422:Tubgcp4	UTSW	2	121189401	nonsense	probably null
R4433:Tubgcp4	UTSW	2	121184473	missense	probably benign	0.01
R4541:Tubgcp4	UTSW	2	121195426	missense	probably benign	0.01
R4670:Tubgcp4	UTSW	2	121173665	nonsense	probably null
R4873:Tubgcp4	UTSW	2	121184849	intron	probably benign
R4877:Tubgcp4	UTSW	2	121189862	missense	probably benign
R5436:Tubgcp4	UTSW	2	121188136	missense	probably damaging	1.00
R5436:Tubgcp4	UTSW	2	121194182	missense	probably benign	0.01
R5566:Tubgcp4	UTSW	2	121184770	missense	possibly damaging	0.61
R6110:Tubgcp4	UTSW	2	121194108	missense	probably benign	0.02
R6700:Tubgcp4	UTSW	2	121189848	missense	probably benign	0.11
R6980:Tubgcp4	UTSW	2	121195465	missense	probably benign	0.28
R6999:Tubgcp4	UTSW	2	121192297	missense	probably damaging	1.00
R7338:Tubgcp4	UTSW	2	121193984	missense	probably benign	0.02
R7388:Tubgcp4	UTSW	2	121189966	critical splice donor site	probably null
R7410:Tubgcp4	UTSW	2	121184409	missense	probably damaging	1.00
R8048:Tubgcp4	UTSW	2	121183500	missense	probably benign	0.00
R8129:Tubgcp4	UTSW	2	121173628	missense	possibly damaging	0.80
R8414:Tubgcp4	UTSW	2	121194153	missense	probably benign	0.02
R9006:Tubgcp4	UTSW	2	121184770	missense	probably benign	0.35
R9050:Tubgcp4	UTSW	2	121173598	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- AGGAACACGACCTTGTAATTGTG -3'
(R):5'- TTCACTGCCTGATAGCACTC -3'

Sequencing Primer
(F):5'- TTGTTAACCAGAATTACCAACCCAG -3'
(R):5'- GATAGCACTCCTGCCCTGTAGAAG -3'

Posted On

2016-06-15