Mutagenetix > Incidental Mutation

Incidental Mutation 'R2126:Lhx6'

229840

Institutional Source

Beutler Lab

Gene Symbol

Lhx6

Ensembl Gene

ENSMUSG00000026890

Gene Name

LIM homeobox protein 6

Synonyms

MMRRC Submission

040129-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.921) question?

Stock #

R2126 (G1)

Quality Score

207

Status

Not validated

Chromosome

Chromosomal Location

36081953-36105408 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 36091324 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 85 (I85T)

Ref Sequence

ENSEMBL: ENSMUSP00000135776 (fasta)

Gene Model

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

AlphaFold

Q9R1R0

Predicted Effect

possibly damaging
Transcript: ENSMUST00000112960
AA Change: I292T

PolyPhen 2 Score 0.469 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000108584
Gene: ENSMUSG00000026890
AA Change: I292T

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: ENSMUST00000112961
AA Change: I263T

PolyPhen 2 Score 0.152 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000108585
Gene: ENSMUSG00000026890
AA Change: I263T

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: ENSMUST00000112963
AA Change: I263T

PolyPhen 2 Score 0.152 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000108587
Gene: ENSMUSG00000026890
AA Change: I263T

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
AA Change: I263T

PolyPhen 2 Score 0.152 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000108590
Gene: ENSMUSG00000026890
AA Change: I263T

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

possibly damaging
Transcript: ENSMUST00000112967
AA Change: I292T

PolyPhen 2 Score 0.469 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000108591
Gene: ENSMUSG00000026890
AA Change: I292T

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

possibly damaging
Transcript: ENSMUST00000136821
AA Change: I85T

PolyPhen 2 Score 0.945 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000135776
Gene: ENSMUSG00000026890
AA Change: I85T

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

Predicted Effect

probably benign
Transcript: ENSMUST00000148852
AA Change: I263T

PolyPhen 2 Score 0.152 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000135693
Gene: ENSMUSG00000026890
AA Change: I263T

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000187180

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 94.8%

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 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: 116 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadac	A	G	3: 60,039,645	T255A	possibly damaging	Het
Acat3	C	T	17: 12,927,407	A230T	probably benign	Het
Acsl1	C	A	8: 46,533,626	P650Q	probably benign	Het
Adgrl3	T	A	5: 81,512,536	I316N	probably damaging	Het
Agrp	G	T	8: 105,566,835	T106K	probably damaging	Het
AI429214	T	A	8: 36,994,208	V170E	probably benign	Het
Akap13	G	A	7: 75,725,304	G1895S	possibly damaging	Het
Alpk2	G	A	18: 65,350,368	Q190*	probably null	Het
Aox3	C	A	1: 58,158,216	Q574K	probably benign	Het
Apeh	A	G	9: 108,085,667	Y702H	probably damaging	Het
Aqp11	A	G	7: 97,737,485	I151T	probably benign	Het
Arhgap28	A	G	17: 67,869,015	V363A	possibly damaging	Het
Arhgef18	A	G	8: 3,451,939	N699S	probably damaging	Het
Asnsd1	A	G	1: 53,347,317	S384P	probably benign	Het
Atl1	G	T	12: 69,931,657		probably null	Het
Atp13a2	A	T	4: 140,995,391	D203V	possibly damaging	Het
Axdnd1	A	T	1: 156,333,214	N164K	probably benign	Het
Bnipl	T	A	3: 95,245,683	I162F	probably damaging	Het
Cacna1d	A	T	14: 30,123,163	L655I	probably damaging	Het
Canx	T	C	11: 50,304,358	I294M	probably damaging	Het
Casz1	T	C	4: 148,946,064	F1180S	probably damaging	Het
Cav3	T	C	6: 112,472,383	Y121H	probably benign	Het
Cd4	A	C	6: 124,870,536	S222A	probably benign	Het
Cds1	T	C	5: 101,812,550	I289T	probably benign	Het
Cep112	T	C	11: 108,508,258	F328L	probably damaging	Het
Ces4a	G	A	8: 105,138,097	G69S	probably damaging	Het
Cfap44	A	T	16: 44,410,475	D273V	probably benign	Het
Clec7a	C	T	6: 129,470,955	G49D	probably benign	Het
Col22a1	G	A	15: 71,857,253	Q599*	probably null	Het
Col6a5	T	A	9: 105,945,600	H186L	unknown	Het
Dclk2	C	T	3: 86,805,639	R503Q	possibly damaging	Het
Dnah12	A	T	14: 26,724,458	R725*	probably null	Het
Dnajc10	G	A	2: 80,350,734		probably null	Het
Edem3	A	T	1: 151,794,731	H337L	possibly damaging	Het
Eif2ak4	A	T	2: 118,422,123	H392L	probably benign	Het
Ercc6l2	G	A	13: 63,848,771	V365I	probably damaging	Het
Fam129a	A	C	1: 151,696,135	E277A	probably damaging	Het
Fam129a	A	G	1: 151,709,133	I494V	possibly damaging	Het
Fan1	T	C	7: 64,346,888	E978G	probably damaging	Het
Fcrl6	C	T	1: 172,599,248	V44M	probably benign	Het
Gaa	G	A	11: 119,270,282	W50*	probably null	Het
Gm10032	T	C	14: 66,792,778		noncoding transcript	Het
Gm10985	CTCTAT	CT	3: 53,845,249		probably null	Het
Gprc5b	G	T	7: 118,984,175	P157Q	probably damaging	Het
Gsdmc3	G	A	15: 63,858,534	Q394*	probably null	Het
Gucd1	A	G	10: 75,512,088	S38P	probably damaging	Het
Higd1a	A	T	9: 121,850,247	I58N	probably damaging	Het
Hmx3	G	C	7: 131,544,549	V329L	possibly damaging	Het
Hnrnpul2	A	T	19: 8,824,438	R337*	probably null	Het
Idua	T	A	5: 108,681,438	H368Q	possibly damaging	Het
Ifih1	A	G	2: 62,623,467	V218A	probably benign	Het
Ip6k1	G	A	9: 108,040,996	E77K	possibly damaging	Het
Kif1b	G	A	4: 149,187,640	S1568L	possibly damaging	Het
Klhl30	T	A	1: 91,358,777		probably null	Het
Lasp1	T	A	11: 97,836,134	D227E	probably benign	Het
Limch1	A	G	5: 67,029,760	D840G	probably damaging	Het
Loxl4	C	G	19: 42,603,963	E385D	probably damaging	Het
Lrrtm4	A	T	6: 80,021,739	I44F	probably damaging	Het
Ltbp2	T	C	12: 84,785,709		probably null	Het
Lyg1	T	C	1: 37,950,674	Y44C	probably damaging	Het
Maats1	T	C	16: 38,341,762	T6A	probably benign	Het
Map1a	A	G	2: 121,298,641	I129V	probably damaging	Het
Med27	C	T	2: 29,524,430	Q150*	probably null	Het
Ms4a5	A	T	19: 11,279,368	I55N	probably damaging	Het
Muc5ac	T	C	7: 141,810,742	S2597P	possibly damaging	Het
Mxd1	A	C	6: 86,651,440		probably null	Het
Myo3a	A	G	2: 22,578,174	D480G	probably benign	Het
Neb	T	C	2: 52,310,638	Y343C	probably damaging	Het
Nrn1	A	C	13: 36,730,206	V34G	probably damaging	Het
Olfr1090	A	T	2: 86,754,452	N95K	probably benign	Het
Olfr1099	T	C	2: 86,959,098	Y120C	possibly damaging	Het
Olfr1302	A	G	2: 111,780,496	M59V	probably damaging	Het
Olfr679	A	G	7: 105,086,615	T300A	probably damaging	Het
Olfr690	C	T	7: 105,329,252	W313*	probably null	Het
Olfr722	A	G	14: 49,895,067	I245T	probably benign	Het
Olfr887	G	T	9: 38,085,276	V147L	probably benign	Het
Pdia4	A	T	6: 47,796,837	V526E	probably damaging	Het
Pdia6	T	C	12: 17,278,545	V167A	probably damaging	Het
Pgk2	A	G	17: 40,207,509	F343L	probably damaging	Het
Piwil1	T	C	5: 128,754,096	V827A	probably damaging	Het
Plag1	A	T	4: 3,904,169	Y341N	possibly damaging	Het
Plch2	T	C	4: 154,998,999	E393G	probably damaging	Het
Ptprg	T	A	14: 12,154,355	M692K	probably benign	Het
Rassf8	G	A	6: 145,815,182	R78H	probably benign	Het
Rif1	GCCACCA	GCCA	2: 52,110,324		probably benign	Het
Rnf213	A	G	11: 119,450,201	Q3556R	probably damaging	Het
Rpa2	T	C	4: 132,768,788		probably null	Het
Rpe	T	G	1: 66,715,980	F174V	possibly damaging	Het
Sbf2	T	C	7: 110,560,295	D36G	probably damaging	Het
Scn2a	T	A	2: 65,752,079	Y1590*	probably null	Het
Slc24a4	T	C	12: 102,222,759	V151A	probably damaging	Het
Slc30a8	A	T	15: 52,295,934	M17L	probably benign	Het
Slit3	T	C	11: 35,688,679	Y1228H	probably damaging	Het
Smad4	G	A	18: 73,662,744	T193M	probably benign	Het
Smtn	T	A	11: 3,530,045	H392L	probably benign	Het
St8sia3	A	G	18: 64,269,674	D128G	probably damaging	Het
Sucla2	A	T	14: 73,592,668	M382L	possibly damaging	Het
Tbx5	A	G	5: 119,836,923	T4A	probably benign	Het
Tdrd5	T	C	1: 156,276,573	R528G	probably damaging	Het
Tex44	T	C	1: 86,427,089	L240P	probably benign	Het
Tns4	A	T	11: 99,080,078		probably null	Het
Trappc10	A	T	10: 78,203,924	V731E	possibly damaging	Het
Ttf1	A	G	2: 29,071,345	K582E	probably damaging	Het
Ttf2	C	A	3: 100,948,193	Q895H	possibly damaging	Het
Ttll6	A	G	11: 96,147,532	E402G	probably damaging	Het
Ttn	A	T	2: 76,890,092		probably null	Het
Ugt8a	T	C	3: 125,875,546	D303G	probably damaging	Het
Ulk1	G	T	5: 110,792,436	A373D	probably benign	Het
Vmn2r13	A	G	5: 109,158,192	S507P	probably benign	Het
Vmn2r19	T	A	6: 123,316,074	D358E	possibly damaging	Het
Vmn2r88	T	C	14: 51,413,807	S201P	probably benign	Het
Zfp36l2	A	G	17: 84,186,975	F78S	probably damaging	Het
Zfp454	A	C	11: 50,873,995	S203R	probably benign	Het
Zfp616	C	A	11: 74,085,403	Q833K	probably benign	Het
Znhit2	A	G	19: 6,062,061	T279A	probably benign	Het
Zswim3	T	A	2: 164,819,993	I131N	probably benign	Het

Other mutations in Lhx6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00088:Lhx6	APN	2	36091716	splice site	probably benign
IGL01391:Lhx6	APN	2	36103465	missense	probably benign	0.00
IGL01413:Lhx6	APN	2	36103516	missense	probably benign	0.24
IGL03154:Lhx6	APN	2	36094443	splice site	probably null
R1546:Lhx6	UTSW	2	36091037	missense	probably benign	0.00
R1630:Lhx6	UTSW	2	36102901	missense	probably damaging	1.00
R1785:Lhx6	UTSW	2	36087458	nonsense	probably null
R1786:Lhx6	UTSW	2	36087458	nonsense	probably null
R1792:Lhx6	UTSW	2	36087375	missense	probably damaging	1.00
R2145:Lhx6	UTSW	2	36087466	missense	probably benign	0.01
R2167:Lhx6	UTSW	2	36103359	missense	probably damaging	1.00
R2393:Lhx6	UTSW	2	36091390	missense	probably benign	0.22
R5102:Lhx6	UTSW	2	36094210	splice site	probably null
R5418:Lhx6	UTSW	2	36087366	critical splice donor site	probably null
R6735:Lhx6	UTSW	2	36091378	missense	probably damaging	0.99
R7462:Lhx6	UTSW	2	36084071	missense	possibly damaging	0.86
R7546:Lhx6	UTSW	2	36103345	critical splice donor site	probably null
R8870:Lhx6	UTSW	2	36105220	unclassified	probably benign
R9192:Lhx6	UTSW	2	36091133	missense	probably benign	0.10
R9667:Lhx6	UTSW	2	36090967	missense	possibly damaging	0.93

Predicted Primers

PCR Primer
(F):5'- CTGCACTCTCAGTAATCAAGGAAAAG -3'
(R):5'- TGTTCGGGACTTGTGACTCC -3'

Sequencing Primer
(F):5'- CTCAGTAATCAAGGAAAAGGGTCAAC -3'
(R):5'- CCGCTCCAAGGATGAAGCTG -3'

Posted On

2014-09-17