Mutagenetix > Incidental Mutation

Incidental Mutation 'R1786:Lhx6'

202781

Institutional Source

Beutler Lab

Gene Symbol

Lhx6

Ensembl Gene

ENSMUSG00000026890

Gene Name

LIM homeobox protein 6

Synonyms

MMRRC Submission

039817-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.930) question?

Stock #

R1786 (G1)

Quality Score

155

Status

Validated

Chromosome

Chromosomal Location

35971965-35995420 bp(-) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

G to T at 35977470 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Stop codon at position 327 (C327*)

Ref Sequence

ENSEMBL: ENSMUSP00000108587 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000112960] [ENSMUST00000112961] [ENSMUST00000112963] [ENSMUST00000112966] [ENSMUST00000112967] [ENSMUST00000136821] [ENSMUST00000148852]

AlphaFold

Q9R1R0

Predicted Effect

probably null
Transcript: ENSMUST00000112960
AA Change: C356*

SMART Domains

Protein: ENSMUSP00000108584
Gene: ENSMUSG00000026890
AA Change: C356*

Domain	Start	End	E-Value	Type
low complexity region	71	94	N/A	INTRINSIC
LIM	98	151	7.34e-13	SMART
LIM	159	213	3.17e-17	SMART
HOX	248	310	1.1e-23	SMART

Predicted Effect

probably null
Transcript: ENSMUST00000112961
AA Change: C327*

SMART Domains

Protein: ENSMUSP00000108585
Gene: ENSMUSG00000026890
AA Change: C327*

Domain	Start	End	E-Value	Type
low complexity region	42	65	N/A	INTRINSIC
LIM	69	122	7.34e-13	SMART
LIM	130	184	3.17e-17	SMART
HOX	219	281	1.1e-23	SMART

Predicted Effect

probably null
Transcript: ENSMUST00000112963
AA Change: C327*

SMART Domains

Protein: ENSMUSP00000108587
Gene: ENSMUSG00000026890
AA Change: C327*

Domain	Start	End	E-Value	Type
low complexity region	42	65	N/A	INTRINSIC
LIM	69	122	7.34e-13	SMART
LIM	130	184	3.17e-17	SMART
HOX	219	281	1.1e-23	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000112966

SMART Domains

Protein: ENSMUSP00000108590
Gene: ENSMUSG00000026890

Domain	Start	End	E-Value	Type
low complexity region	42	65	N/A	INTRINSIC
LIM	69	122	7.34e-13	SMART
LIM	130	184	3.17e-17	SMART
HOX	219	281	1.1e-23	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000112967

SMART Domains

Protein: ENSMUSP00000108591
Gene: ENSMUSG00000026890

Domain	Start	End	E-Value	Type
low complexity region	71	94	N/A	INTRINSIC
LIM	98	151	7.34e-13	SMART
LIM	159	213	3.17e-17	SMART
HOX	248	310	1.1e-23	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000136821

SMART Domains

Protein: ENSMUSP00000135776
Gene: ENSMUSG00000026890

Domain	Start	End	E-Value	Type
LIM	10	64	3.17e-17	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000148852

SMART Domains

Protein: ENSMUSP00000135693
Gene: ENSMUSG00000026890

Domain	Start	End	E-Value	Type
low complexity region	42	65	N/A	INTRINSIC
LIM	69	122	7.34e-13	SMART
LIM	130	184	3.17e-17	SMART
HOX	219	281	1.1e-23	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000185171

Meta Mutation Damage Score

0.9754

Coding Region Coverage

1x: 97.5%
3x: 96.9%
10x: 95.3%
20x: 92.4%

Validation Efficiency

97% (98/101)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of a large protein family that contains the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein has tandem LIM domains as well as a DNA-binding homeodomain. The protein functions as a transcription factor involved in embryogenesis and head development and is highly expressed in neural crest derived mesenchyme cells. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2017]
PHENOTYPE: Homozygous mutation of this gene results in impaired migration and specification of cortical interneurons, postnatal lethality and weakness. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 93 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A2ml1	T	A	6: 128,553,223 (GRCm39)	N178I	probably damaging	Het
Abcc4	G	A	14: 118,790,761 (GRCm39)	R749C	probably damaging	Het
Acot11	T	C	4: 106,619,232 (GRCm39)	E201G	probably damaging	Het
Akap13	G	T	7: 75,261,182 (GRCm39)	A1269S	probably benign	Het
Aldh4a1	T	C	4: 139,371,439 (GRCm39)	V451A	probably benign	Het
Aopep	T	A	13: 63,357,963 (GRCm39)	C656S	probably benign	Het
Aox3	A	G	1: 58,209,002 (GRCm39)	H845R	probably damaging	Het
Asb6	G	A	2: 30,717,088 (GRCm39)	R46W	probably damaging	Het
Bpifb6	T	C	2: 153,748,781 (GRCm39)	F259S	probably damaging	Het
Cad	T	A	5: 31,215,416 (GRCm39)	F76I	probably damaging	Het
Camk2b	T	C	11: 5,927,880 (GRCm39)	E390G	probably benign	Het
Cars1	C	A	7: 143,146,211 (GRCm39)	R71M	probably damaging	Het
Ccdc170	T	G	10: 4,469,043 (GRCm39)	I197S	probably benign	Het
Ccn4	G	A	15: 66,778,338 (GRCm39)	C53Y	probably damaging	Het
Cdc20b	A	T	13: 113,217,668 (GRCm39)	K362N	probably damaging	Het
Cntrl	CAGAG	CAG	2: 35,012,818 (GRCm39)		probably null	Het
Cpd	T	C	11: 76,683,624 (GRCm39)	D1045G	probably benign	Het
Crocc	T	C	4: 140,749,113 (GRCm39)	D1564G	probably damaging	Het
Csf1r	A	T	18: 61,262,149 (GRCm39)	M802L	probably damaging	Het
Dctn4	T	C	18: 60,679,407 (GRCm39)		probably null	Het
Dnah5	A	G	15: 28,313,932 (GRCm39)	Q1916R	probably damaging	Het
Dpysl2	A	G	14: 67,100,114 (GRCm39)		probably benign	Het
Dync2h1	A	G	9: 7,081,084 (GRCm39)	Y2871H	probably damaging	Het
Fam221b	T	A	4: 43,665,537 (GRCm39)	H307L	probably damaging	Het
Foxn4	C	T	5: 114,401,193 (GRCm39)	D37N	probably damaging	Het
Gemin4	G	C	11: 76,101,876 (GRCm39)	P962A	probably damaging	Het
Gm9797	T	C	10: 11,485,069 (GRCm39)		noncoding transcript	Het
Golim4	A	T	3: 75,815,456 (GRCm39)	V116D	probably damaging	Het
Gper1	C	T	5: 139,412,477 (GRCm39)	P274L	probably damaging	Het
Gpr132	A	G	12: 112,816,023 (GRCm39)	S268P	probably damaging	Het
Gtpbp2	T	C	17: 46,472,128 (GRCm39)	M21T	probably benign	Het
Hivep1	C	T	13: 42,337,262 (GRCm39)	A2447V	possibly damaging	Het
Ift20	G	A	11: 78,430,860 (GRCm39)	E68K	probably damaging	Het
Insrr	G	A	3: 87,717,879 (GRCm39)		probably null	Het
Kcnh8	T	C	17: 53,200,961 (GRCm39)	V465A	probably damaging	Het
Kif5c	T	A	2: 49,648,817 (GRCm39)		probably benign	Het
Kmt2a	G	A	9: 44,730,972 (GRCm39)		probably benign	Het
Lifr	A	G	15: 7,211,337 (GRCm39)	D625G	possibly damaging	Het
Llgl1	T	C	11: 60,598,066 (GRCm39)	V370A	probably benign	Het
Lman1	A	T	18: 66,124,653 (GRCm39)	M362K	probably damaging	Het
Lmtk2	C	T	5: 144,111,806 (GRCm39)	T842I	possibly damaging	Het
Lpin3	T	A	2: 160,738,729 (GRCm39)	L227*	probably null	Het
Ltv1	C	G	10: 13,058,280 (GRCm39)		probably benign	Het
Magel2	A	T	7: 62,027,486 (GRCm39)	H130L	unknown	Het
Mettl17	A	T	14: 52,126,192 (GRCm39)		probably benign	Het
Mnx1	T	A	5: 29,679,187 (GRCm39)	S299C	unknown	Het
Mov10	A	T	3: 104,725,432 (GRCm39)	I59N	possibly damaging	Het
Myo7b	T	C	18: 32,127,950 (GRCm39)	I581V	probably benign	Het
Ncdn	T	A	4: 126,639,066 (GRCm39)		probably null	Het
Ndufa4	A	T	6: 11,900,574 (GRCm39)	V37E	probably benign	Het
Nhsl1	T	G	10: 18,400,412 (GRCm39)	L546R	probably benign	Het
Nop9	T	C	14: 55,988,599 (GRCm39)	L347P	probably damaging	Het
Nrp1	A	T	8: 129,224,997 (GRCm39)	E782D	probably damaging	Het
Ntrk3	G	A	7: 78,127,683 (GRCm39)		probably benign	Het
Or1j13	A	G	2: 36,370,059 (GRCm39)	S28P	possibly damaging	Het
Or2z8	A	G	8: 72,812,280 (GRCm39)	Y252C	probably damaging	Het
Or8g53	A	T	9: 39,683,791 (GRCm39)	C102S	probably benign	Het
Osbpl6	T	A	2: 76,416,558 (GRCm39)	I546K	probably damaging	Het
Pard6g	T	C	18: 80,160,523 (GRCm39)	V212A	probably damaging	Het
Pknox2	A	G	9: 36,820,980 (GRCm39)	V294A	probably damaging	Het
Plekha1	T	C	7: 130,493,983 (GRCm39)	V106A	probably benign	Het
Plekha6	C	A	1: 133,207,103 (GRCm39)		probably null	Het
Ptgdr	A	T	14: 45,096,036 (GRCm39)	Y225*	probably null	Het
Ptpn22	A	G	3: 103,781,368 (GRCm39)	I90V	probably damaging	Het
Pygb	C	T	2: 150,658,692 (GRCm39)	T372I	probably damaging	Het
Pzp	T	C	6: 128,468,124 (GRCm39)		probably null	Het
Qrich2	C	T	11: 116,332,275 (GRCm39)	G2307D	probably damaging	Het
Rfwd3	A	T	8: 112,024,034 (GRCm39)	V96E	probably benign	Het
Senp1	T	A	15: 97,973,848 (GRCm39)	T132S	probably benign	Het
Slc9a4	T	G	1: 40,646,901 (GRCm39)		probably null	Het
Slfn9	T	A	11: 82,872,133 (GRCm39)	I868F	probably damaging	Het
St3gal6	T	C	16: 58,296,234 (GRCm39)	D137G	probably damaging	Het
Synj1	G	T	16: 90,761,405 (GRCm39)	A687D	probably damaging	Het
Syt4	A	G	18: 31,576,496 (GRCm39)		probably benign	Het
Tacc1	A	T	8: 25,654,509 (GRCm39)	N271K	probably damaging	Het
Tdrd6	T	C	17: 43,935,724 (GRCm39)	T1775A	probably benign	Het
Tecpr1	T	A	5: 144,145,463 (GRCm39)	T595S	probably benign	Het
Tjp3	T	A	10: 81,113,888 (GRCm39)	M457L	possibly damaging	Het
Tmem200a	T	A	10: 25,869,825 (GRCm39)	H148L	probably damaging	Het
Trappc8	A	G	18: 20,967,997 (GRCm39)		probably null	Het
Txk	T	A	5: 72,853,922 (GRCm39)	T472S	probably damaging	Het
Ubr4	T	A	4: 139,151,256 (GRCm39)	M1897K	probably damaging	Het
Uggt2	A	G	14: 119,298,788 (GRCm39)	L391P	probably damaging	Het
Uncx	T	C	5: 139,533,302 (GRCm39)	S456P	probably benign	Het
Vps13b	A	G	15: 35,879,937 (GRCm39)	Y3004C	probably damaging	Het
Vps35l	T	C	7: 118,393,798 (GRCm39)	Y516H	probably damaging	Het
Zbtb46	C	T	2: 181,033,224 (GRCm39)	C479Y	probably damaging	Het
Zc3h7a	A	T	16: 10,968,469 (GRCm39)	Y503*	probably null	Het
Zdhhc13	T	A	7: 48,474,392 (GRCm39)	L548Q	possibly damaging	Het
Zfp236	T	C	18: 82,639,429 (GRCm39)	M1225V	probably benign	Het
Zfp280d	T	C	9: 72,215,287 (GRCm39)	F133L	probably damaging	Het
Zfp503	A	T	14: 22,035,588 (GRCm39)	C443S	possibly damaging	Het
Zfyve26	T	A	12: 79,315,208 (GRCm39)	I1423F	possibly damaging	Het

Other mutations in Lhx6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00088:Lhx6	APN	2	35,981,728 (GRCm39)	splice site	probably benign
IGL01391:Lhx6	APN	2	35,993,477 (GRCm39)	missense	probably benign	0.00
IGL01413:Lhx6	APN	2	35,993,528 (GRCm39)	missense	probably benign	0.24
IGL03154:Lhx6	APN	2	35,984,455 (GRCm39)	splice site	probably null
R1546:Lhx6	UTSW	2	35,981,049 (GRCm39)	missense	probably benign	0.00
R1630:Lhx6	UTSW	2	35,992,913 (GRCm39)	missense	probably damaging	1.00
R1785:Lhx6	UTSW	2	35,977,470 (GRCm39)	nonsense	probably null
R1792:Lhx6	UTSW	2	35,977,387 (GRCm39)	missense	probably damaging	1.00
R2126:Lhx6	UTSW	2	35,981,336 (GRCm39)	missense	possibly damaging	0.94
R2145:Lhx6	UTSW	2	35,977,478 (GRCm39)	missense	probably benign	0.01
R2167:Lhx6	UTSW	2	35,993,371 (GRCm39)	missense	probably damaging	1.00
R2393:Lhx6	UTSW	2	35,981,402 (GRCm39)	missense	probably benign	0.22
R5102:Lhx6	UTSW	2	35,984,222 (GRCm39)	splice site	probably null
R5418:Lhx6	UTSW	2	35,977,378 (GRCm39)	critical splice donor site	probably null
R6735:Lhx6	UTSW	2	35,981,390 (GRCm39)	missense	probably damaging	0.99
R7462:Lhx6	UTSW	2	35,974,083 (GRCm39)	missense	possibly damaging	0.86
R7546:Lhx6	UTSW	2	35,993,357 (GRCm39)	critical splice donor site	probably null
R8870:Lhx6	UTSW	2	35,995,232 (GRCm39)	unclassified	probably benign
R9192:Lhx6	UTSW	2	35,981,145 (GRCm39)	missense	probably benign	0.10
R9667:Lhx6	UTSW	2	35,980,979 (GRCm39)	missense	possibly damaging	0.93

Predicted Primers

PCR Primer
(F):5'- TGGCATGGTAACCACTCAGTG -3'
(R):5'- GTGTGGACTTAGCAGTGAGC -3'

Sequencing Primer
(F):5'- CACTCAGTGGTAGGGAATGCTG -3'
(R):5'- CCTGATAAACCCTTCAAGTGTGTAGC -3'

Posted On

2014-06-23