Mutagenetix > Incidental Mutation

Incidental Mutation 'R1942:Six5'

216288

Institutional Source

Beutler Lab

Gene Symbol

Six5

Ensembl Gene

ENSMUSG00000040841

Gene Name

sine oculis-related homeobox 5

Synonyms

Dmahp, TrexBF, MDMAHP

MMRRC Submission

039960-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.779) question?

Stock #

R1942 (G1)

Quality Score

223

Status

Validated

Chromosome

Chromosomal Location

18828519-18832474 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 18830858 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Valine at position 495 (A495V)

Ref Sequence

ENSEMBL: ENSMUSP00000045973 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000032568] [ENSMUST00000049454] [ENSMUST00000108473] [ENSMUST00000108474] [ENSMUST00000127433] [ENSMUST00000141380] [ENSMUST00000154199]

AlphaFold

P70178

Predicted Effect

probably benign
Transcript: ENSMUST00000032568

SMART Domains

Protein: ENSMUSP00000032568
Gene: ENSMUSG00000030409

Domain	Start	End	E-Value	Type
low complexity region	5	31	N/A	INTRINSIC
S_TKc	71	339	6.5e-87	SMART
S_TK_X	340	407	3.6e-11	SMART
Pfam:DMPK_coil	472	532	2.8e-25	PFAM
low complexity region	590	613	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000049454
AA Change: A495V

PolyPhen 2 Score 0.679 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000045973
Gene: ENSMUSG00000040841
AA Change: A495V

Domain	Start	End	E-Value	Type
coiled coil region	14	48	N/A	INTRINSIC
Pfam:SIX1_SD	79	189	1.4e-43	PFAM
HOX	194	256	3.11e-14	SMART
low complexity region	300	313	N/A	INTRINSIC
low complexity region	347	358	N/A	INTRINSIC
low complexity region	429	442	N/A	INTRINSIC
low complexity region	564	574	N/A	INTRINSIC
low complexity region	620	639	N/A	INTRINSIC
low complexity region	674	687	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000108473

SMART Domains

Protein: ENSMUSP00000104113
Gene: ENSMUSG00000030409

Domain	Start	End	E-Value	Type
low complexity region	5	31	N/A	INTRINSIC
S_TKc	71	339	1.36e-84	SMART
S_TK_X	340	407	7.5e-9	SMART
Pfam:DMPK_coil	472	532	2.2e-28	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000108474

SMART Domains

Protein: ENSMUSP00000104114
Gene: ENSMUSG00000030409

Domain	Start	End	E-Value	Type
low complexity region	5	31	N/A	INTRINSIC
S_TKc	71	336	2.57e-76	SMART
Pfam:DMPK_coil	446	506	2.4e-28	PFAM
low complexity region	564	587	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126264

Predicted Effect

probably benign
Transcript: ENSMUST00000127433

SMART Domains

Protein: ENSMUSP00000115597
Gene: ENSMUSG00000085601

Domain	Start	End	E-Value	Type
Blast:HLH	20	57	1e-17	BLAST

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132115

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000142725

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000140742

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000143938

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148380

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000135839

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137219

Predicted Effect

probably benign
Transcript: ENSMUST00000141380

SMART Domains

Protein: ENSMUSP00000115575
Gene: ENSMUSG00000085601

Domain	Start	End	E-Value	Type
HLH	20	74	6.84e-1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000154199

SMART Domains

Protein: ENSMUSP00000118459
Gene: ENSMUSG00000030409

Domain	Start	End	E-Value	Type
low complexity region	5	31	N/A	INTRINSIC
S_TKc	71	339	1.36e-84	SMART
S_TK_X	340	402	5.3e-9	SMART
Pfam:DMPK_coil	467	527	2.3e-28	PFAM

Meta Mutation Damage Score

0.1443

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.6%
20x: 93.7%

Validation Efficiency

100% (75/75)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this gene are a cause of branchiootorenal syndrome type 2. [provided by RefSeq, Jul 2009]
PHENOTYPE: Homozygous null mutants exhibit a high incidence of progressive cataracts with background-dependent penetrance. Heterozygotes exhibit a similar phenotype, but with reduced incidence and severity. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930407I10Rik	A	T	15: 81,949,625 (GRCm39)	Y1174F	probably damaging	Het
Ahnak	A	G	19: 8,992,447 (GRCm39)	E4577G	probably damaging	Het
Anapc4	T	C	5: 53,004,056 (GRCm39)	V291A	probably benign	Het
Apba2	A	G	7: 64,345,218 (GRCm39)	E136G	possibly damaging	Het
Arhgap20	C	A	9: 51,742,998 (GRCm39)	Q279K	probably benign	Het
B3galnt1	A	T	3: 69,483,258 (GRCm39)	M1K	probably null	Het
C4bp	C	A	1: 130,583,804 (GRCm39)		probably benign	Het
Catsperg1	G	A	7: 28,906,232 (GRCm39)	T157I	possibly damaging	Het
Cfap90	A	C	13: 68,761,090 (GRCm39)	I171L	probably benign	Het
Chrm1	T	A	19: 8,655,637 (GRCm39)	M114K	probably damaging	Het
Clasp1	A	G	1: 118,429,078 (GRCm39)	E329G	possibly damaging	Het
Clrn2	A	C	5: 45,611,337 (GRCm39)	Y62S	probably benign	Het
Col12a1	T	G	9: 79,542,748 (GRCm39)	D2339A	probably damaging	Het
Copa	T	A	1: 171,939,455 (GRCm39)	L564Q	probably damaging	Het
Cpeb2	C	A	5: 43,392,596 (GRCm39)		probably benign	Het
Dhx57	A	T	17: 80,572,573 (GRCm39)	M647K	probably damaging	Het
Diaph3	C	T	14: 87,378,556 (GRCm39)		probably benign	Het
Eomes	A	G	9: 118,313,716 (GRCm39)	D587G	probably benign	Het
Gm5142	T	A	14: 59,416,156 (GRCm39)	M1L	probably benign	Het
Gnl2	A	G	4: 124,923,957 (GRCm39)	I12V	probably benign	Het
Gprin1	C	T	13: 54,887,752 (GRCm39)	C174Y	probably benign	Het
Grin2b	A	T	6: 135,709,730 (GRCm39)	V1272E	possibly damaging	Het
Hdac9	A	G	12: 34,479,544 (GRCm39)	L227S	probably damaging	Het
Helz	T	A	11: 107,493,318 (GRCm39)	L247Q	probably benign	Het
Hs6st1	T	C	1: 36,107,803 (GRCm39)	V22A	probably benign	Het
Hspg2	C	A	4: 137,269,863 (GRCm39)	A2304E	possibly damaging	Het
Htr3a	T	C	9: 48,819,911 (GRCm39)	Y73C	probably damaging	Het
Il1rap	A	C	16: 26,541,205 (GRCm39)	E482A	probably damaging	Het
Itsn2	T	A	12: 4,689,670 (GRCm39)	L581*	probably null	Het
Msmb	A	G	14: 31,870,034 (GRCm39)	E2G	probably benign	Het
Muc19	T	C	15: 91,776,666 (GRCm39)		noncoding transcript	Het
Muc4	A	C	16: 32,569,460 (GRCm39)	L173F	probably damaging	Het
Muc5b	A	T	7: 141,411,421 (GRCm39)	S1456C	unknown	Het
Mylip	A	T	13: 45,560,172 (GRCm39)	I203F	probably damaging	Het
Nckap5	A	T	1: 125,952,039 (GRCm39)	D1504E	probably damaging	Het
Neil1	C	G	9: 57,053,891 (GRCm39)	R143P	probably benign	Het
Nlrp2	T	A	7: 5,325,447 (GRCm39)	T742S	probably damaging	Het
Nme8	A	G	13: 19,859,978 (GRCm39)	V214A	probably damaging	Het
Nsun7	C	T	5: 66,441,588 (GRCm39)	T419I	probably benign	Het
Nup210l	G	A	3: 90,058,544 (GRCm39)	E648K	probably benign	Het
Or10g6	T	A	9: 39,934,031 (GRCm39)	L114H	probably damaging	Het
Or10g6	T	C	9: 39,934,048 (GRCm39)	Y120H	probably damaging	Het
Or2y1c	T	C	11: 49,360,981 (GRCm39)	M1T	probably null	Het
Or8s2	A	G	15: 98,276,445 (GRCm39)	L182P	probably damaging	Het
Parp11	A	C	6: 127,447,663 (GRCm39)		probably null	Het
Pomgnt1	G	T	4: 116,012,472 (GRCm39)		probably null	Het
Ppp1r14c	T	C	10: 3,413,417 (GRCm39)	I150T	probably damaging	Het
Psd4	A	G	2: 24,295,805 (GRCm39)	E908G	probably damaging	Het
Psmd6	A	T	14: 14,116,442 (GRCm38)	V91E	probably damaging	Het
Ptk2b	A	T	14: 66,406,830 (GRCm39)	V634D	probably damaging	Het
Rapgef6	A	G	11: 54,548,089 (GRCm39)	I753V	possibly damaging	Het
Rbm45	G	A	2: 76,205,823 (GRCm39)		probably null	Het
Ric1	A	G	19: 29,578,416 (GRCm39)		probably benign	Het
Sh3rf2	A	G	18: 42,282,689 (GRCm39)	K416E	probably damaging	Het
Slc27a6	T	A	18: 58,689,870 (GRCm39)	M112K	probably damaging	Het
Slc5a4a	T	C	10: 75,983,422 (GRCm39)	S20P	unknown	Het
Smg1	A	G	7: 117,757,326 (GRCm39)		probably benign	Het
Sntb2	G	A	8: 107,737,984 (GRCm39)	A511T	probably damaging	Het
Stk31	A	T	6: 49,416,061 (GRCm39)	N622I	probably damaging	Het
Sulf1	T	C	1: 12,918,397 (GRCm39)	F38S	probably damaging	Het
Szt2	G	T	4: 118,249,817 (GRCm39)	T521K	probably benign	Het
Terf1	G	T	1: 15,876,038 (GRCm39)	R46I	probably benign	Het
Tmem245	A	G	4: 56,923,511 (GRCm39)		probably benign	Het
Tmigd1	T	C	11: 76,804,905 (GRCm39)		probably null	Het
Ugcg	C	T	4: 59,207,798 (GRCm39)	P46S	probably benign	Het
Umod	A	G	7: 119,076,155 (GRCm39)	Y204H	probably damaging	Het
Vcan	T	A	13: 89,851,543 (GRCm39)	Q1139L	probably benign	Het
Vmn1r85	T	A	7: 12,818,668 (GRCm39)	T159S	possibly damaging	Het
Vmn2r103	T	A	17: 20,032,562 (GRCm39)	S779T	probably benign	Het
Vmn2r27	C	T	6: 124,200,722 (GRCm39)	A412T	probably damaging	Het
Zc3h12d	A	C	10: 7,729,077 (GRCm39)	D147A	probably damaging	Het
Zfp800	A	T	6: 28,243,272 (GRCm39)	D564E	probably benign	Het
Zfp932	A	G	5: 110,154,853 (GRCm39)	E17G	probably damaging	Het

Other mutations in Six5

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00975:Six5	APN	7	18,831,603 (GRCm39)	missense	probably damaging	1.00
IGL01543:Six5	APN	7	18,830,272 (GRCm39)	missense	possibly damaging	0.46
IGL02643:Six5	APN	7	18,831,455 (GRCm39)	missense	probably benign	0.14
IGL03137:Six5	APN	7	18,831,072 (GRCm39)	unclassified	probably benign
R0243:Six5	UTSW	7	18,830,947 (GRCm39)	splice site	probably null
R0410:Six5	UTSW	7	18,830,381 (GRCm39)	missense	probably damaging	1.00
R2055:Six5	UTSW	7	18,829,154 (GRCm39)	missense	possibly damaging	0.78
R3726:Six5	UTSW	7	18,830,855 (GRCm39)	missense	possibly damaging	0.86
R4801:Six5	UTSW	7	18,830,894 (GRCm39)	missense	probably benign	0.19
R4802:Six5	UTSW	7	18,830,894 (GRCm39)	missense	probably benign	0.19
R4898:Six5	UTSW	7	18,829,096 (GRCm39)	missense	probably damaging	1.00
R6150:Six5	UTSW	7	18,831,446 (GRCm39)	missense	probably benign	0.34
R6432:Six5	UTSW	7	18,830,696 (GRCm39)	missense	probably damaging	1.00
R6667:Six5	UTSW	7	18,830,494 (GRCm39)	missense	probably benign	0.00
R6736:Six5	UTSW	7	18,828,916 (GRCm39)	missense	possibly damaging	0.83
R7101:Six5	UTSW	7	18,828,784 (GRCm39)	missense	probably benign	0.01
R7253:Six5	UTSW	7	18,828,901 (GRCm39)	missense	probably damaging	1.00
R7402:Six5	UTSW	7	18,828,968 (GRCm39)	missense	probably damaging	1.00
R7719:Six5	UTSW	7	18,830,803 (GRCm39)	missense	probably damaging	0.99
R8089:Six5	UTSW	7	18,828,797 (GRCm39)	missense	probably damaging	1.00
R8748:Six5	UTSW	7	18,829,049 (GRCm39)	missense	probably benign	0.00
R9182:Six5	UTSW	7	18,830,932 (GRCm39)	missense	probably benign
R9283:Six5	UTSW	7	18,829,148 (GRCm39)	missense	probably damaging	1.00
RF007:Six5	UTSW	7	18,828,862 (GRCm39)	missense	probably benign	0.00
RF030:Six5	UTSW	7	18,828,725 (GRCm39)	unclassified	probably benign
RF037:Six5	UTSW	7	18,828,725 (GRCm39)	unclassified	probably benign

Predicted Primers

PCR Primer
(F):5'- GGACTACTGGAGAGGAAATCCC -3'
(R):5'- CAGTAGGCTTAACTCCAAGAGAC -3'

Sequencing Primer
(F):5'- TGCCCCAAGTAGTCCCAG -3'
(R):5'- CTTAACTCCAAGAGACTATCAGGTGG -3'

Posted On

2014-08-01