Mutagenetix > Incidental Mutation

Incidental Mutation 'R1806:Lhx1'

203481

Institutional Source

Beutler Lab

Gene Symbol

Lhx1

Ensembl Gene

ENSMUSG00000018698

Gene Name

LIM homeobox protein 1

Synonyms

Lim1

MMRRC Submission

039835-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1806 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

84409110-84416361 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 84414967 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Glutamine at position 12 (L12Q)

Ref Sequence

ENSEMBL: ENSMUSP00000018842 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000018842] [ENSMUST00000092827] [ENSMUST00000184646]

AlphaFold

P63006

Predicted Effect

probably damaging
Transcript: ENSMUST00000018842
AA Change: L12Q

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000018842
Gene: ENSMUSG00000018698
AA Change: L12Q

Domain	Start	End	E-Value	Type
LIM	3	54	5.51e-17	SMART
LIM	62	117	4.24e-18	SMART
low complexity region	137	156	N/A	INTRINSIC
HOX	180	242	1.33e-22	SMART
low complexity region	315	327	N/A	INTRINSIC
low complexity region	349	367	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000092827

SMART Domains

Protein: ENSMUSP00000090503
Gene: ENSMUSG00000018698

Domain	Start	End	E-Value	Type
LIM	18	73	4.24e-18	SMART
low complexity region	93	112	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126072

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128121

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134800

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176503

SMART Domains

Protein: ENSMUSP00000135334
Gene: ENSMUSG00000018698

Domain	Start	End	E-Value	Type
Pfam:Homeobox	1	17	5.3e-6	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000184646

SMART Domains

Protein: ENSMUSP00000138899
Gene: ENSMUSG00000018698

Domain	Start	End	E-Value	Type
low complexity region	46	65	N/A	INTRINSIC
HOX	89	151	6.8e-25	SMART
low complexity region	224	236	N/A	INTRINSIC
low complexity region	258	276	N/A	INTRINSIC

Meta Mutation Damage Score

0.4786

Coding Region Coverage

1x: 97.5%
3x: 96.8%
10x: 94.9%
20x: 91.2%

Validation Efficiency

96% (77/80)

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 which contains the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein is a transcription factor important for the development of the renal and urogenital systems. This gene is a candidate for Mayer-Rokitansky-Kuster-Hauser syndrome, a disorder characterized by anomalies in the female genital tract. [provided by RefSeq, Dec 2010]
PHENOTYPE: Homozygotes for targeted null mutations are small, fail to develop head structures anterior to rhombomere 3 in the hindbrain, lack kidneys and gonads, and show aberrant trajectories of limb motor axons. Most mutants die around embryonic day 10. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadacl2fm3	T	C	3: 59,784,571 (GRCm39)	L348P	probably damaging	Het
Adamts15	C	A	9: 30,816,111 (GRCm39)	C616F	probably damaging	Het
Adarb1	T	C	10: 77,158,099 (GRCm39)	N116S	probably damaging	Het
Add2	C	T	6: 86,095,639 (GRCm39)	S437L	probably damaging	Het
Adra1d	T	A	2: 131,388,069 (GRCm39)	R495S	probably benign	Het
Agk	C	T	6: 40,364,429 (GRCm39)	T309I	probably damaging	Het
Aqr	T	C	2: 113,992,133 (GRCm39)	Y81C	probably damaging	Het
Bak1	G	A	17: 27,240,242 (GRCm39)	Q142*	probably null	Het
Bckdha	A	G	7: 25,330,845 (GRCm39)	V307A	probably damaging	Het
Camk2n2	C	A	16: 20,438,948 (GRCm39)	G72V	probably benign	Het
Cd276	A	T	9: 58,434,845 (GRCm39)		probably benign	Het
Cd2ap	G	A	17: 43,149,649 (GRCm39)	Q122*	probably null	Het
Cdan1	T	A	2: 120,561,907 (GRCm39)		probably benign	Het
Cdh3	T	C	8: 107,263,547 (GRCm39)	S156P	probably benign	Het
Chil4	T	A	3: 106,117,959 (GRCm39)		probably benign	Het
Col11a1	C	T	3: 113,951,791 (GRCm39)	R1074C	probably damaging	Het
Depp1	G	A	6: 116,628,683 (GRCm39)	V9M	possibly damaging	Het
Fcrlb	T	C	1: 170,735,096 (GRCm39)	T344A	probably benign	Het
Fras1	T	A	5: 96,861,829 (GRCm39)		probably benign	Het
Fras1	G	T	5: 96,912,835 (GRCm39)	V3380F	possibly damaging	Het
Galnt9	A	G	5: 110,767,119 (GRCm39)	D530G	possibly damaging	Het
Gja10	A	T	4: 32,601,135 (GRCm39)	S416R	probably benign	Het
Gm10549	T	A	18: 33,603,841 (GRCm39)	V108E	unknown	Het
Hook3	A	T	8: 26,558,687 (GRCm39)	L59Q	probably damaging	Het
Hpf1	T	A	8: 61,353,154 (GRCm39)	D178E	probably benign	Het
Hsd17b7	T	C	1: 169,788,698 (GRCm39)	N173S	possibly damaging	Het
Hsph1	A	G	5: 149,553,454 (GRCm39)	F236L	probably damaging	Het
Kcnk12	G	T	17: 88,053,537 (GRCm39)	T375K	probably benign	Het
Klra3	A	T	6: 130,304,033 (GRCm39)	S220T	probably damaging	Het
Lnx1	A	G	5: 74,766,710 (GRCm39)	L468P	probably damaging	Het
Ltbp3	T	A	19: 5,803,970 (GRCm39)	C827*	probably null	Het
Mical1	C	T	10: 41,354,210 (GRCm39)	A53V	probably damaging	Het
Mmp10	A	T	9: 7,506,502 (GRCm39)	H326L	probably benign	Het
Mpl	A	T	4: 118,300,729 (GRCm39)	M600K	possibly damaging	Het
Muc5b	T	A	7: 141,419,230 (GRCm39)	D4004E	possibly damaging	Het
Myo5b	A	T	18: 74,710,680 (GRCm39)	H98L	possibly damaging	Het
Nbeal1	A	G	1: 60,323,251 (GRCm39)	T2110A	probably damaging	Het
Nedd4l	C	A	18: 65,345,862 (GRCm39)	R825S	probably damaging	Het
Ntn4	C	T	10: 93,543,215 (GRCm39)	R314W	probably damaging	Het
Or4k35	A	T	2: 111,100,622 (GRCm39)	I30N	possibly damaging	Het
Or52e19	T	A	7: 102,959,432 (GRCm39)	L168Q	probably damaging	Het
Or8k41	A	T	2: 86,313,483 (GRCm39)	I201N	probably damaging	Het
Otog	A	T	7: 45,940,361 (GRCm39)		probably null	Het
Parp2	T	A	14: 51,056,836 (GRCm39)	L320H	probably damaging	Het
Poglut3	T	C	9: 53,307,150 (GRCm39)	Y365H	probably damaging	Het
Pola2	C	T	19: 5,993,250 (GRCm39)		probably null	Het
Poln	A	T	5: 34,264,494 (GRCm39)		probably benign	Het
Pomt1	T	A	2: 32,131,680 (GRCm39)	V123E	probably damaging	Het
Prom2	T	C	2: 127,374,802 (GRCm39)	Y578C	probably damaging	Het
Prss23	T	C	7: 89,159,599 (GRCm39)	T157A	probably damaging	Het
Sdk1	T	A	5: 141,598,950 (GRCm39)	V205E	probably damaging	Het
Sdk1	A	G	5: 142,147,681 (GRCm39)	K1771R	probably benign	Het
Sidt1	A	T	16: 44,102,234 (GRCm39)	S309T	possibly damaging	Het
Sirpa	T	A	2: 129,457,432 (GRCm39)	F169I	probably damaging	Het
Slc8a1	T	C	17: 81,955,916 (GRCm39)	N374S	probably damaging	Het
Sp110	C	T	1: 85,523,831 (GRCm39)		probably null	Het
Stard9	A	G	2: 120,509,934 (GRCm39)		probably null	Het
Synpr	A	G	14: 13,563,082 (GRCm38)	N105S	probably damaging	Het
Tbc1d16	T	C	11: 119,046,927 (GRCm39)	Y440C	probably damaging	Het
Trabd	A	G	15: 88,969,824 (GRCm39)	I313V	possibly damaging	Het
Trappc10	T	C	10: 78,046,610 (GRCm39)	R430G	probably damaging	Het
Trim50	A	G	5: 135,387,743 (GRCm39)	E145G	probably benign	Het
Uba2	A	T	7: 33,862,624 (GRCm39)	F105I	probably damaging	Het
Uba3	A	G	6: 97,176,230 (GRCm39)	V92A	possibly damaging	Het
Uhmk1	T	C	1: 170,038,628 (GRCm39)	K153R	probably damaging	Het
Vmn2r3	T	C	3: 64,194,810 (GRCm39)	K8R	possibly damaging	Het
Vmn2r3	T	A	3: 64,182,893 (GRCm39)	M269L	probably benign	Het
Xpot	G	T	10: 121,443,543 (GRCm39)		probably benign	Het
Zfp128	A	G	7: 12,624,949 (GRCm39)	Y439C	probably benign	Het
Zfy1	T	A	Y: 725,620 (GRCm39)	H715L	possibly damaging	Het
Zmym1	A	C	4: 126,941,872 (GRCm39)	L839V	probably damaging	Het

Other mutations in Lhx1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00757:Lhx1	APN	11	84,410,478 (GRCm39)	missense	probably damaging	0.97
R1346:Lhx1	UTSW	11	84,412,905 (GRCm39)	missense	possibly damaging	0.55
R1565:Lhx1	UTSW	11	84,410,647 (GRCm39)	missense	probably benign	0.00
R2148:Lhx1	UTSW	11	84,410,647 (GRCm39)	missense	probably benign	0.00
R2449:Lhx1	UTSW	11	84,412,564 (GRCm39)	missense	probably damaging	1.00
R3721:Lhx1	UTSW	11	84,412,654 (GRCm39)	missense	probably damaging	1.00
R3793:Lhx1	UTSW	11	84,412,726 (GRCm39)	missense	probably benign	0.01
R4940:Lhx1	UTSW	11	84,410,735 (GRCm39)	nonsense	probably null
R5178:Lhx1	UTSW	11	84,411,214 (GRCm39)	missense	possibly damaging	0.69
R5877:Lhx1	UTSW	11	84,413,065 (GRCm39)	missense	probably damaging	1.00
R6366:Lhx1	UTSW	11	84,413,034 (GRCm39)	missense	probably damaging	1.00
R6551:Lhx1	UTSW	11	84,412,739 (GRCm39)	missense	probably benign	0.23
R7060:Lhx1	UTSW	11	84,411,108 (GRCm39)	critical splice donor site	probably null
R7106:Lhx1	UTSW	11	84,412,903 (GRCm39)	missense	probably benign	0.00
R7133:Lhx1	UTSW	11	84,410,746 (GRCm39)	missense	probably benign	0.00
R7161:Lhx1	UTSW	11	84,410,698 (GRCm39)	missense	probably damaging	1.00
R7290:Lhx1	UTSW	11	84,412,703 (GRCm39)	missense	probably damaging	0.96
R8843:Lhx1	UTSW	11	84,410,455 (GRCm39)	missense	probably benign	0.03

Predicted Primers

PCR Primer
(F):5'- CTGCCCTAGTAAAAGGCAGC -3'
(R):5'- CCCTTTTGATTTGCTAGTACGG -3'

Sequencing Primer
(F):5'- AGACCTCTGATCCGAAGCTG -3'
(R):5'- TCGACTCTAATTGCCCTG -3'

Posted On

2014-06-23