Mutagenetix > Incidental Mutation

Incidental Mutation 'R2167:Lhx6'

235521

Institutional Source

Beutler Lab

Gene Symbol

Lhx6

Ensembl Gene

ENSMUSG00000026890

Gene Name

LIM homeobox protein 6

Synonyms

MMRRC Submission

040170-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.926) question?

Stock #

R2167 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

35971965-35995420 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 35993371 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Leucine at position 80 (R80L)

Ref Sequence

ENSEMBL: ENSMUSP00000135693 (fasta)

Gene Model

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

AlphaFold

Q9R1R0

Predicted Effect

probably damaging
Transcript: ENSMUST00000112960
AA Change: R109L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000108584
Gene: ENSMUSG00000026890
AA Change: R109L

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: R80L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000108585
Gene: ENSMUSG00000026890
AA Change: R80L

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: R80L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000108587
Gene: ENSMUSG00000026890
AA Change: R80L

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: ENSMUST00000112966
AA Change: R80L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000108590
Gene: ENSMUSG00000026890
AA Change: R80L

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: ENSMUST00000112967
AA Change: R109L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000108591
Gene: ENSMUSG00000026890
AA Change: R109L

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

noncoding transcript
Transcript: ENSMUST00000137436

Predicted Effect

probably damaging
Transcript: ENSMUST00000148852
AA Change: R80L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000135693
Gene: ENSMUSG00000026890
AA Change: R80L

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: ENSMUST00000187180

Meta Mutation Damage Score

0.9140

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.5%

Validation Efficiency

98% (57/58)

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: 55 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca13	C	T	11: 9,238,532 (GRCm39)	T710M	probably benign	Het
Acan	A	G	7: 78,749,705 (GRCm39)	E1492G	probably benign	Het
Acsl1	A	G	8: 46,986,627 (GRCm39)	D638G	possibly damaging	Het
Acsl6	C	A	11: 54,217,983 (GRCm39)	T207K	probably benign	Het
Ahnak	A	T	19: 8,988,858 (GRCm39)	K3381*	probably null	Het
Art1	T	C	7: 101,756,031 (GRCm39)	V74A	probably damaging	Het
Bhmt2	A	T	13: 93,799,012 (GRCm39)	W270R	probably benign	Het
Calm2	T	C	17: 87,742,573 (GRCm39)	T118A	probably benign	Het
Ccdc88b	G	T	19: 6,831,452 (GRCm39)	Q497K	possibly damaging	Het
Ccne2	A	T	4: 11,197,249 (GRCm39)	M183L	probably benign	Het
Cdc42bpg	A	G	19: 6,367,707 (GRCm39)	I1026V	probably damaging	Het
Celsr2	T	C	3: 108,320,509 (GRCm39)	T768A	probably damaging	Het
Cog5	T	C	12: 31,887,288 (GRCm39)	F470L	probably damaging	Het
Cpne5	T	C	17: 29,381,306 (GRCm39)	D374G	probably damaging	Het
Disp2	A	C	2: 118,622,166 (GRCm39)	E966A	probably damaging	Het
Dmrtc2	C	T	7: 24,573,344 (GRCm39)		probably benign	Het
Eif2b3	T	A	4: 116,885,737 (GRCm39)	I93N	probably damaging	Het
Elfn2	C	A	15: 78,556,646 (GRCm39)	V634L	probably benign	Het
Fasl	T	G	1: 161,614,707 (GRCm39)	S119R	probably benign	Het
Foxp2	C	G	6: 15,437,901 (GRCm39)	P701A	probably damaging	Het
Helz	T	A	11: 107,563,790 (GRCm39)		probably benign	Het
Kctd6	T	C	14: 8,222,683 (GRCm38)	V175A	probably benign	Het
Leo1	A	G	9: 75,352,991 (GRCm39)	N178S	probably benign	Het
Man1a2	A	G	3: 100,499,216 (GRCm39)	L406P	probably damaging	Het
Mapkap1	T	C	2: 34,487,494 (GRCm39)	F231L	probably damaging	Het
Mknk2	A	G	10: 80,504,535 (GRCm39)	Y256H	probably damaging	Het
Msh6	A	G	17: 88,296,911 (GRCm39)	T1203A	probably damaging	Het
Nbeal2	T	C	9: 110,467,376 (GRCm39)	Y604C	probably damaging	Het
Ncam1	G	T	9: 49,479,781 (GRCm39)	Q66K	probably benign	Het
Nsd2	T	A	5: 34,040,263 (GRCm39)	H933Q	probably damaging	Het
Or10h5	T	A	17: 33,434,542 (GRCm39)	I262F	probably damaging	Het
Or13p3	T	C	4: 118,567,252 (GRCm39)	V216A	probably benign	Het
Or2d3c	A	G	7: 106,525,797 (GRCm39)	Y290H	probably damaging	Het
Or5h23	T	A	16: 58,905,949 (GRCm39)	K299I	probably benign	Het
Pappa	A	C	4: 65,074,682 (GRCm39)	D412A	probably damaging	Het
Ptch1	T	G	13: 63,672,773 (GRCm39)	E944A	probably benign	Het
Rassf6	C	T	5: 90,751,797 (GRCm39)	E308K	probably damaging	Het
Rb1	T	C	14: 73,449,091 (GRCm39)	T680A	probably damaging	Het
Rfpl4	T	A	7: 5,113,852 (GRCm39)	I104F	probably damaging	Het
Rin2	C	T	2: 145,702,366 (GRCm39)	T354I	probably benign	Het
Rnase6	A	C	14: 51,367,974 (GRCm39)	D122A	probably benign	Het
Rsf1	GGCG	GGCGACGGCAGCG	7: 97,229,113 (GRCm39)		probably benign	Het
Sec31b	G	A	19: 44,531,792 (GRCm39)	T39I	possibly damaging	Het
Slc12a1	A	G	2: 125,015,601 (GRCm39)	I385V	probably damaging	Het
Slc6a17	A	T	3: 107,398,817 (GRCm39)	Y261*	probably null	Het
Supt6	G	A	11: 78,098,993 (GRCm39)	P1626L	possibly damaging	Het
Tbx15	A	G	3: 99,233,771 (GRCm39)		probably benign	Het
Telo2	A	G	17: 25,329,792 (GRCm39)	V240A	probably benign	Het
Trhr	C	T	15: 44,092,638 (GRCm39)	L292F	probably damaging	Het
Trps1	G	A	15: 50,695,126 (GRCm39)	L340F	possibly damaging	Het
Ube2e1	T	C	14: 18,284,429 (GRCm38)		probably benign	Het
Yeats2	T	C	16: 20,032,151 (GRCm39)		probably benign	Het
Zbtb39	G	A	10: 127,578,844 (GRCm39)	E473K	probably benign	Het
Zfp235	T	A	7: 23,840,387 (GRCm39)	S269T	possibly damaging	Het
Zfp580	C	A	7: 5,056,063 (GRCm39)	P141Q	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
R1786: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
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'- CTGTTTGGGAACACTTGCCC -3'
(R):5'- GAGGAAACCAGATTCAACTCTGAG -3'

Sequencing Primer
(F):5'- TTTGGGAACACTTGCCCAAAGC -3'
(R):5'- AGATTCAACTCTGAGTACTCGGC -3'

Posted On

2014-10-01