Mutagenetix > Incidental Mutation

Incidental Mutation 'RF003:Six3'

602665

Institutional Source

Beutler Lab

Gene Symbol

Six3

Ensembl Gene

ENSMUSG00000038805

Gene Name

sine oculis-related homeobox 3

Synonyms

E130112M24Rik

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

RF003 (G1)

Quality Score

154.468

Status

Not validated

Chromosome

Chromosomal Location

85921036-85933619 bp(+) (GRCm39)

Type of Mutation

small insertion (1 aa in frame mutation)

DNA Base Change (assembly)

GCG to GCGTCG at 85928798 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000135312 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000162695] [ENSMUST00000175898] [ENSMUST00000176081]

AlphaFold

Q62233

Predicted Effect

probably benign
Transcript: ENSMUST00000162695

SMART Domains

Protein: ENSMUSP00000125169
Gene: ENSMUSG00000038805

Domain	Start	End	E-Value	Type
low complexity region	30	71	N/A	INTRINSIC
HOX	208	269	1.26e-14	SMART
low complexity region	294	310	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000175898

SMART Domains

Protein: ENSMUSP00000135677
Gene: ENSMUSG00000038805

Domain	Start	End	E-Value	Type
low complexity region	30	71	N/A	INTRINSIC
HOX	208	269	1.26e-14	SMART
low complexity region	294	310	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000176081

SMART Domains

Protein: ENSMUSP00000135312
Gene: ENSMUSG00000038805

Domain	Start	End	E-Value	Type
low complexity region	51	92	N/A	INTRINSIC
Pfam:SIX1_SD	109	223	6e-47	PFAM
HOX	229	290	6.5e-17	SMART
low complexity region	315	331	N/A	INTRINSIC

Coding Region Coverage

1x: 99.8%
3x: 99.7%
10x: 99.2%
20x: 98.1%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the sine oculis homeobox transcription factor family. The encoded protein plays a role in eye development. Mutations in this gene have been associated with holoprosencephaly type 2. [provided by RefSeq, Oct 2009]
PHENOTYPE: Mice homozygous for disruptions of this gene die at birth with anterior structures of the head and brain undeveloped. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930433I11Rik	AACC	A	7: 40,642,479 (GRCm39)		probably benign	Het
A630073D07Rik	A	C	6: 132,604,406 (GRCm39)	L13R	unknown	Het
Alg9	GGC	GGCCGC	9: 50,686,727 (GRCm39)		probably benign	Het
Arb2a	A	T	13: 77,982,794 (GRCm39)	I135L	possibly damaging	Het
Arc	G	C	15: 74,543,980 (GRCm39)	T81S	probably benign	Het
Atad5	A	T	11: 80,002,386 (GRCm39)	K1059N	probably damaging	Het
Bdp1	C	A	13: 100,196,957 (GRCm39)	V1143F	probably benign	Het
Bdp1	C	A	13: 100,196,958 (GRCm39)	Q1142H	probably benign	Het
Ccdc33	T	C	9: 57,965,574 (GRCm39)	S583G	probably benign	Het
Cd109	TTAT	TTATTTATTTATATAT	9: 78,619,813 (GRCm39)		probably benign	Het
Cep192	A	T	18: 67,971,027 (GRCm39)	R1009S	probably benign	Het
Clvs2	T	A	10: 33,498,921 (GRCm39)	H3L	probably damaging	Het
Cnot6	T	C	11: 49,593,440 (GRCm39)	M14V	probably benign	Het
Colec10	A	G	15: 54,325,787 (GRCm39)	R206G	possibly damaging	Het
Dennd6a	T	C	14: 26,350,689 (GRCm39)	I598T	probably damaging	Het
Dmrt2	T	C	19: 25,655,498 (GRCm39)	S366P	probably damaging	Het
Dnmt1	AGTTCCTACCTCGTT	AGTTCCTACCTCGTTTTGGGGGCGGAGCACCGTTCCTACCTCGTT	9: 20,821,427 (GRCm39)		probably null	Het
Efhb	T	C	17: 53,707,919 (GRCm39)	D748G	probably damaging	Het
Etl4	C	T	2: 20,524,729 (GRCm39)	Q21*	probably null	Het
Flywch1	CCACTCCTGGTGT	CCACTCCTGGTGTGGGGAGGCTACGTACTCACACACTCCTGGTGT	17: 23,981,140 (GRCm39)		probably null	Het
Fmn1	ACCTCC	ACCTCCCCCTCC	2: 113,356,131 (GRCm39)		probably benign	Het
Fsip2	T	A	2: 82,821,865 (GRCm39)	M5866K	probably benign	Het
Gab3	CTT	CTTATT	X: 74,043,612 (GRCm39)		probably null	Het
Garin5a	C	CGGAGGGAGGAAGGCTGGATCCTGGATACCTGGGTA	7: 44,149,951 (GRCm39)		probably null	Het
Gnl2	T	A	4: 124,937,518 (GRCm39)		probably null	Het
Grip2	C	T	6: 91,760,574 (GRCm39)	R341Q	probably benign	Het
Hmcn1	T	A	1: 150,500,312 (GRCm39)	H3960L	probably damaging	Het
Igkv6-25	T	A	6: 70,192,762 (GRCm39)	Y56*	probably null	Het
Il12a	A	T	3: 68,602,562 (GRCm39)	T102S	probably benign	Het
Il1a	T	A	2: 129,144,852 (GRCm39)	I189F	possibly damaging	Het
Inpp4b	T	A	8: 82,696,150 (GRCm39)	Y361*	probably null	Het
Iqcf4	CTTTTCCTTTTCCTTTT	CTTTTCCTTTTCCTTTTCCTTTTCCTTTTCCTTTTCATTTTCCTTTTCCTTTT	9: 106,447,806 (GRCm39)		probably benign	Het
Irag2	AGCACATTG	AGCACATTGTGCACATTG	6: 145,119,509 (GRCm39)		probably benign	Het
Krt1	AAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCAC	AAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCAC	15: 101,758,813 (GRCm39)		probably benign	Het
Las1l	AGTGG	AGTGGTGG	X: 94,984,422 (GRCm39)		probably benign	Het
Lrrc8d	T	C	5: 105,960,507 (GRCm39)	Y306H	probably damaging	Het
Mamld1	AGC	AGCCGC	X: 70,162,426 (GRCm39)		probably benign	Het
Map1a	CTCCAGCTCCAGCTCCAGCTCCA	CTCCAGCTCCAGCTCCAGCTCCAGCTCCAGATCCAGCTCCAGCTCCAGCTCCA	2: 121,136,777 (GRCm39)		probably benign	Het
Map1b	G	T	13: 99,567,258 (GRCm39)	A1821E	unknown	Het
Maz	A	G	7: 126,624,669 (GRCm39)	C284R	probably damaging	Het
Med23	A	G	10: 24,779,683 (GRCm39)	H920R	probably damaging	Het
Megf10	CCAGCAGCAGCAGCAGCAGCAG	CCAGCAGCAGCAGCAGCAG	18: 57,427,099 (GRCm39)		probably benign	Het
Mmp14	C	T	14: 54,676,471 (GRCm39)	R339*	probably null	Het
Mroh9	T	G	1: 162,885,630 (GRCm39)	K334T	probably damaging	Het
Nab1	A	T	1: 52,518,441 (GRCm39)	C320S	probably damaging	Het
Noto	T	C	6: 85,401,192 (GRCm39)	S74P	probably benign	Het
Nudt4	T	C	10: 95,385,236 (GRCm39)	N152D	possibly damaging	Het
Nup155	T	TTTTG	15: 8,148,660 (GRCm39)		probably benign	Het
Nusap1	AGCTGAGA	AGCTGAGATACACGTTAGCAGTGAGGAGCAGGCTGAGA	2: 119,458,084 (GRCm39)		probably benign	Het
Or10al2	A	C	17: 37,983,749 (GRCm39)	K278N	probably damaging	Het
Or2d4	T	A	7: 106,543,855 (GRCm39)	M118L	probably damaging	Het
Or2t48	CA	C	11: 58,419,983 (GRCm39)		probably null	Het
Or51f1e	GTTAT	GTTATTAT	7: 102,747,512 (GRCm39)			Het
Or51f1e	TTA	TTAGTA	7: 102,747,513 (GRCm39)		probably null	Het
Or7g16	T	C	9: 18,726,778 (GRCm39)	T271A	probably benign	Het
Or9a7	T	C	6: 40,521,296 (GRCm39)	I206V	probably benign	Het
Plxnc1	T	C	10: 94,630,306 (GRCm39)	Y1531C	probably damaging	Het
Pnma8b	TGA	TGAAGA	7: 16,679,941 (GRCm39)		probably benign	Het
Rp1	A	G	1: 4,414,917 (GRCm39)	V2065A	probably damaging	Het
Sbp	AAGATGCTGACAACA	AAGATGCTGACAACAGAGATGCTGACAACA	17: 24,164,343 (GRCm39)		probably benign	Het
Sepsecs	G	A	5: 52,804,533 (GRCm39)	T379M	probably benign	Het
Sfswap	GGCC	GGCCCACTCTGCC	5: 129,646,828 (GRCm39)		probably benign	Het
Tfeb	C	T	17: 48,099,003 (GRCm39)	T259I	possibly damaging	Het
Tgoln1	A	AAACTCAG	6: 72,593,335 (GRCm39)		probably null	Het
Tmem94	G	A	11: 115,686,958 (GRCm39)	V1108M	probably damaging	Het
Usp35	T	C	7: 96,971,303 (GRCm39)	K297E	possibly damaging	Het
Vcpkmt	T	A	12: 69,629,598 (GRCm39)	T55S	possibly damaging	Het
Zfp384	GCCCAGGCCCAG	GCCCAGGCCCAGTCCCAGGCCCAG	6: 125,013,446 (GRCm39)		probably benign	Het
Zfp384	GCCCAGGCCCAGGCCCAGGCCCAG	GCCCAGGCCCAGTCCCAGGCCCAGGCCCAGGCCCAG	6: 125,013,434 (GRCm39)		probably benign	Het
Zfp384	GGCCC	GGCCCTGGCCCAAGCCC	6: 125,013,439 (GRCm39)		probably benign	Het
Zfp407	A	T	18: 84,227,688 (GRCm39)	S1974T	probably benign	Het
Zfp677	T	C	17: 21,617,704 (GRCm39)	S254P	probably damaging	Het

Other mutations in Six3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL03096:Six3	APN	17	85,929,365 (GRCm39)	missense	possibly damaging	0.78
IGL03397:Six3	APN	17	85,929,074 (GRCm39)	missense	probably damaging	1.00
FR4304:Six3	UTSW	17	85,928,796 (GRCm39)	small insertion	probably benign
FR4340:Six3	UTSW	17	85,928,784 (GRCm39)	small insertion	probably benign
FR4449:Six3	UTSW	17	85,928,790 (GRCm39)	small insertion	probably benign
FR4548:Six3	UTSW	17	85,928,791 (GRCm39)	small insertion	probably benign
FR4589:Six3	UTSW	17	85,928,793 (GRCm39)	small insertion	probably benign
FR4737:Six3	UTSW	17	85,928,786 (GRCm39)	small insertion	probably benign
FR4737:Six3	UTSW	17	85,928,785 (GRCm39)	small insertion	probably benign
FR4737:Six3	UTSW	17	85,928,796 (GRCm39)	small insertion	probably benign
FR4737:Six3	UTSW	17	85,928,793 (GRCm39)	small insertion	probably benign
FR4737:Six3	UTSW	17	85,928,791 (GRCm39)	small insertion	probably benign
FR4737:Six3	UTSW	17	85,928,790 (GRCm39)	small insertion	probably benign
FR4976:Six3	UTSW	17	85,928,799 (GRCm39)	small insertion	probably benign
FR4976:Six3	UTSW	17	85,928,786 (GRCm39)	small insertion	probably benign
R0238:Six3	UTSW	17	85,928,818 (GRCm39)	missense	probably damaging	1.00
R1264:Six3	UTSW	17	85,929,285 (GRCm39)	missense	probably damaging	0.96
R2903:Six3	UTSW	17	85,931,283 (GRCm39)	missense	probably damaging	0.96
R2916:Six3	UTSW	17	85,929,061 (GRCm39)	missense	probably benign	0.25
R4994:Six3	UTSW	17	85,928,720 (GRCm39)	missense	possibly damaging	0.91
R5393:Six3	UTSW	17	85,931,270 (GRCm39)	missense	possibly damaging	0.93
R6524:Six3	UTSW	17	85,929,398 (GRCm39)	missense	probably damaging	1.00
R8998:Six3	UTSW	17	85,931,164 (GRCm39)	missense	probably benign	0.01
R8999:Six3	UTSW	17	85,931,164 (GRCm39)	missense	probably benign	0.01
RF010:Six3	UTSW	17	85,928,783 (GRCm39)	small insertion	probably benign
RF011:Six3	UTSW	17	85,928,796 (GRCm39)	small insertion	probably benign
RF012:Six3	UTSW	17	85,928,796 (GRCm39)	small insertion	probably benign
RF014:Six3	UTSW	17	85,928,784 (GRCm39)	small insertion	probably benign
RF015:Six3	UTSW	17	85,928,798 (GRCm39)	small insertion	probably benign
RF022:Six3	UTSW	17	85,928,784 (GRCm39)	small insertion	probably benign
RF054:Six3	UTSW	17	85,928,783 (GRCm39)	small insertion	probably benign

Predicted Primers

PCR Primer
(F):5'- TGAATCTTGACTCGGCCGTG -3'
(R):5'- GTTTGTTGATGGCCTCGCAC -3'

Sequencing Primer
(F):5'- GTGGGTGTCCCTTACGTCC -3'
(R):5'- CGATGTCGCCCGTCTCC -3'

Posted On

2019-12-04