Mutagenetix > Incidental Mutation

Incidental Mutation 'R1792:Lhx6'

201804

Institutional Source

Beutler Lab

Gene Symbol

Lhx6

Ensembl Gene

ENSMUSG00000026890

Gene Name

LIM homeobox protein 6

Synonyms

MMRRC Submission

039822-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.930) question?

Stock #

R1792 (G1)

Quality Score

186

Status

Not validated

Chromosome

Chromosomal Location

35971965-35995420 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 35977387 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Aspartic acid at position 355 (G355D)

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 damaging
Transcript: ENSMUST00000112960
AA Change: G384D

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

SMART Domains

Protein: ENSMUSP00000108584
Gene: ENSMUSG00000026890
AA Change: G384D

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 damaging
Transcript: ENSMUST00000112961
AA Change: G355D

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

SMART Domains

Protein: ENSMUSP00000108585
Gene: ENSMUSG00000026890
AA Change: G355D

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 damaging
Transcript: ENSMUST00000112963
AA Change: G355D

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

SMART Domains

Protein: ENSMUSP00000108587
Gene: ENSMUSG00000026890
AA Change: G355D

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

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 95.2%
20x: 92.4%

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: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca6	C	T	11: 110,074,870 (GRCm39)	V1398I	probably benign	Het
Ackr3	A	T	1: 90,142,620 (GRCm39)	N360Y	probably benign	Het
Acr	T	G	15: 89,457,346 (GRCm39)	M198R	probably benign	Het
Adamts14	A	T	10: 61,054,277 (GRCm39)	M585K	probably benign	Het
Adgrb3	A	T	1: 25,267,552 (GRCm39)	C853S	probably damaging	Het
Arhgef28	G	T	13: 98,067,694 (GRCm39)	S1410R	probably benign	Het
Asprv1	T	A	6: 86,605,354 (GRCm39)	F67I	possibly damaging	Het
Atp8b4	T	A	2: 126,167,214 (GRCm39)	Y1095F	probably benign	Het
Cadps	A	G	14: 12,449,802 (GRCm38)	S1136P	possibly damaging	Het
Ccdc57	T	C	11: 120,788,707 (GRCm39)	Q380R	possibly damaging	Het
Cdc45	A	T	16: 18,626,090 (GRCm39)	D142E	probably benign	Het
Cs	A	T	10: 128,195,948 (GRCm39)	N386Y	possibly damaging	Het
Dsc3	A	T	18: 20,120,055 (GRCm39)	V201E	probably damaging	Het
Dusp26	G	T	8: 31,581,963 (GRCm39)	R19L	probably benign	Het
Esyt3	C	A	9: 99,240,169 (GRCm39)	E92*	probably null	Het
Ext2	T	C	2: 93,534,890 (GRCm39)	N625D	probably damaging	Het
Flvcr2	A	T	12: 85,793,929 (GRCm39)	K102*	probably null	Het
Fmnl2	T	A	2: 52,932,329 (GRCm39)	S103T	possibly damaging	Het
Fmo4	T	A	1: 162,621,859 (GRCm39)	I451F	probably benign	Het
Gak	A	T	5: 108,733,397 (GRCm39)	Y47*	probably null	Het
Gbp10	A	T	5: 105,372,166 (GRCm39)	L198Q	probably damaging	Het
Gm11559	T	A	11: 99,755,755 (GRCm39)	S135T	unknown	Het
Gm14496	A	T	2: 181,637,946 (GRCm39)	D340V	probably benign	Het
Grin2a	T	C	16: 9,810,259 (GRCm39)	T47A	possibly damaging	Het
Gtf2ird1	A	T	5: 134,395,790 (GRCm39)		probably null	Het
Herc4	T	A	10: 63,081,680 (GRCm39)	M1K	probably null	Het
Hirip3	T	A	7: 126,461,792 (GRCm39)	V29E	probably damaging	Het
Hs3st5	A	G	10: 36,708,720 (GRCm39)	D85G	probably benign	Het
Htt	T	A	5: 35,064,543 (GRCm39)	S2981T	probably damaging	Het
Iho1	A	C	9: 108,282,111 (GRCm39)	S526A	possibly damaging	Het
Il20ra	G	A	10: 19,635,384 (GRCm39)	V542I	probably damaging	Het
Itgb2l	C	A	16: 96,226,282 (GRCm39)	C603F	probably damaging	Het
Klhl41	A	C	2: 69,501,146 (GRCm39)	K202N	probably benign	Het
Lct	G	A	1: 128,255,679 (GRCm39)	S121F	possibly damaging	Het
Limk2	A	G	11: 3,308,236 (GRCm39)	V121A	probably benign	Het
Med1	T	G	11: 98,048,109 (GRCm39)	K896Q	probably damaging	Het
Muc6	A	G	7: 141,214,371 (GRCm39)	F2789S	probably benign	Het
Nemf	T	A	12: 69,359,343 (GRCm39)	Y997F	probably damaging	Het
Nrap	A	G	19: 56,367,590 (GRCm39)	S296P	probably benign	Het
Nrxn1	T	C	17: 90,896,252 (GRCm39)	N961D	probably damaging	Het
Odad2	T	C	18: 7,286,743 (GRCm39)	T163A	probably benign	Het
Or1r1	A	C	11: 73,874,673 (GRCm39)	S254A	probably benign	Het
Or6c207	A	T	10: 129,105,112 (GRCm39)	F27I	probably benign	Het
Or6y1	T	C	1: 174,276,303 (GRCm39)	V38A	probably benign	Het
Parp14	G	A	16: 35,677,130 (GRCm39)	A946V	probably benign	Het
Pdk4	T	A	6: 5,489,166 (GRCm39)	H247L	probably damaging	Het
Pkd1l3	T	A	8: 110,359,237 (GRCm39)	V866E	probably damaging	Het
Pla2g4e	G	A	2: 119,998,955 (GRCm39)	P803L	probably damaging	Het
Pnisr	T	C	4: 21,860,968 (GRCm39)	V217A	possibly damaging	Het
Pole4	G	A	6: 82,629,720 (GRCm39)	P34L	unknown	Het
Pole4	G	T	6: 82,629,721 (GRCm39)	P34T	unknown	Het
Ptchd3	G	A	11: 121,732,377 (GRCm39)	W422*	probably null	Het
Rab1b	C	T	19: 5,150,513 (GRCm39)	A167T	probably benign	Het
Rasal1	T	C	5: 120,802,821 (GRCm39)	M359T	probably benign	Het
Rexo4	T	C	2: 26,850,248 (GRCm39)	N310D	probably benign	Het
Rgma	C	T	7: 73,067,585 (GRCm39)	T280M	probably damaging	Het
Rnaset2a	A	T	17: 8,364,408 (GRCm39)	I43N	probably damaging	Het
Rtcb	A	T	10: 85,778,446 (GRCm39)	V399E	probably damaging	Het
Scd4	T	G	19: 44,326,013 (GRCm39)	Y122*	probably null	Het
Sirt6	T	C	10: 81,462,355 (GRCm39)	I15V	possibly damaging	Het
Slamf8	A	T	1: 172,415,526 (GRCm39)	V104E	possibly damaging	Het
Slc12a4	A	G	8: 106,678,475 (GRCm39)	I285T	possibly damaging	Het
Slc25a13	G	A	6: 6,115,104 (GRCm39)	A207V	possibly damaging	Het
Slc6a21	T	C	7: 44,930,155 (GRCm39)	S185P	probably benign	Het
Smarcc2	A	C	10: 128,299,740 (GRCm39)	N135T	probably damaging	Het
Susd6	T	C	12: 80,921,065 (GRCm39)	S221P	probably damaging	Het
Syne1	C	T	10: 4,990,975 (GRCm39)	G8418D	probably damaging	Het
Tasor2	T	C	13: 3,640,559 (GRCm39)	K193E	possibly damaging	Het
Tbc1d7	C	T	13: 43,318,853 (GRCm39)	V95I	probably benign	Het
Tcerg1l	T	C	7: 137,963,595 (GRCm39)	D225G	probably benign	Het
Tfip11	A	T	5: 112,477,263 (GRCm39)	I82F	possibly damaging	Het
Tmem41a	C	T	16: 21,755,731 (GRCm39)	G192S	probably null	Het
Trrap	G	A	5: 144,790,396 (GRCm39)	A3619T	possibly damaging	Het
Tspoap1	G	A	11: 87,656,707 (GRCm39)		probably null	Het
Wfdc21	T	C	11: 83,637,883 (GRCm39)	S11P	probably benign	Het
Zc2hc1b	A	T	10: 13,044,474 (GRCm39)	V63E	probably 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
R1786:Lhx6	UTSW	2	35,977,470 (GRCm39)	nonsense	probably null
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'- CACACAAGTAGCTGCTCTGATG -3'
(R):5'- TAGCACTGTAGCCAGCTCAG -3'

Sequencing Primer
(F):5'- ACAAGTAGCTGCTCTGATGACTGC -3'
(R):5'- CTCCAAGTTAGTGATCAGAGCACG -3'

Posted On

2014-06-23