Mutagenetix > Incidental Mutation

Incidental Mutation 'R5877:Lhx1'

455613

Institutional Source

Beutler Lab

Gene Symbol

Lhx1

Ensembl Gene

ENSMUSG00000018698

Gene Name

LIM homeobox protein 1

Synonyms

Lim1

MMRRC Submission

044083-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5877 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

84409110-84416361 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 84413065 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Tyrosine at position 30 (D30Y)

Ref Sequence

ENSEMBL: ENSMUSP00000090503 (fasta)

Gene Model

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

AlphaFold

P63006

Predicted Effect

probably damaging
Transcript: ENSMUST00000018842
AA Change: D74Y

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

SMART Domains

Protein: ENSMUSP00000018842
Gene: ENSMUSG00000018698
AA Change: D74Y

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 damaging
Transcript: ENSMUST00000092827
AA Change: D30Y

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

SMART Domains

Protein: ENSMUSP00000090503
Gene: ENSMUSG00000018698
AA Change: D30Y

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

0.5173

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.2%
20x: 94.7%

Validation Efficiency

97% (68/70)

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: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam6b	A	T	12: 113,453,822 (GRCm39)	H213L	probably damaging	Het
Alk	A	G	17: 72,274,521 (GRCm39)	W597R	probably damaging	Het
Ark2n	G	T	18: 77,730,902 (GRCm39)		probably null	Het
Ash1l	G	A	3: 88,888,891 (GRCm39)	V257I	probably benign	Het
Atp9b	C	T	18: 80,796,004 (GRCm39)	V957I	probably benign	Het
Birc2	A	C	9: 7,849,347 (GRCm39)	C576G	probably damaging	Het
Brca2	T	C	5: 150,466,686 (GRCm39)	M2150T	possibly damaging	Het
C3ar1	T	G	6: 122,827,581 (GRCm39)	D212A	probably benign	Het
Cacna1s	T	C	1: 136,028,405 (GRCm39)	F914S	probably damaging	Het
Camk1d	T	C	2: 5,570,476 (GRCm39)	I62V	probably benign	Het
Caskin1	T	C	17: 24,724,239 (GRCm39)	M1009T	possibly damaging	Het
Casp2	A	G	6: 42,253,571 (GRCm39)		probably benign	Het
Cd2bp2	T	A	7: 126,793,971 (GRCm39)	Y106F	probably damaging	Het
Celsr3	G	A	9: 108,722,926 (GRCm39)	C2763Y	probably damaging	Het
Cyp2g1	T	G	7: 26,516,065 (GRCm39)	L310V	possibly damaging	Het
Dusp22	G	A	13: 30,891,944 (GRCm39)	V99M	probably damaging	Het
Elp1	A	T	4: 56,787,807 (GRCm39)	W375R	probably damaging	Het
Fam131b	G	A	6: 42,297,913 (GRCm39)	S92L	probably benign	Het
Fbxw10	A	T	11: 62,748,542 (GRCm39)	N390Y	probably damaging	Het
Flg2	A	T	3: 93,110,756 (GRCm39)	H928L	unknown	Het
Gapdhs	T	C	7: 30,431,772 (GRCm39)	T280A	probably damaging	Het
Hdac11	A	G	6: 91,134,524 (GRCm39)	K50E	probably damaging	Het
Hif3a	G	T	7: 16,785,071 (GRCm39)	A181E	probably damaging	Het
Itgb8	A	G	12: 119,166,271 (GRCm39)	S87P	probably benign	Het
Klhl12	T	A	1: 134,411,558 (GRCm39)	Y302*	probably null	Het
Mrpl40	A	G	16: 18,691,135 (GRCm39)	Y148H	probably damaging	Het
Myh13	A	T	11: 67,244,484 (GRCm39)	H1007L	possibly damaging	Het
Nhlrc2	T	C	19: 56,559,016 (GRCm39)	I167T	probably damaging	Het
Nxpe3	A	T	16: 55,686,564 (GRCm39)	I148K	probably damaging	Het
Odf2l	A	G	3: 144,834,771 (GRCm39)		probably null	Het
Otud7b	C	T	3: 96,059,277 (GRCm39)	R347*	probably null	Het
P3h4	G	T	11: 100,304,843 (GRCm39)	H181Q	probably benign	Het
P4htm	T	A	9: 108,460,932 (GRCm39)	Y180F	possibly damaging	Het
Pcna-ps2	A	G	19: 9,261,463 (GRCm39)	I241V	probably benign	Het
Pcnx2	T	C	8: 126,480,467 (GRCm39)	S1947G	probably damaging	Het
Piezo2	T	C	18: 63,247,005 (GRCm39)	I336V	probably benign	Het
Plcd1	T	C	9: 118,905,240 (GRCm39)	D157G	probably damaging	Het
Plekhm2	A	C	4: 141,367,004 (GRCm39)	I212S	probably damaging	Het
Pmvk	G	T	3: 89,371,676 (GRCm39)	C57F	probably benign	Het
Pole	T	C	5: 110,480,329 (GRCm39)	S91P	probably benign	Het
Ppargc1b	C	G	18: 61,442,164 (GRCm39)	D591H	probably damaging	Het
Ppp4r3b	A	T	11: 29,159,356 (GRCm39)	D570V	probably damaging	Het
Pxdn	T	A	12: 30,053,045 (GRCm39)	I1074N	probably damaging	Het
Ralgapa2	A	T	2: 146,230,489 (GRCm39)	D1025E	probably damaging	Het
Ralgps1	A	G	2: 33,133,640 (GRCm39)		probably benign	Het
Rasal1	C	T	5: 120,817,135 (GRCm39)		probably benign	Het
Rps2	A	T	17: 24,939,890 (GRCm39)		probably benign	Het
Scn7a	G	C	2: 66,530,217 (GRCm39)	Y709*	probably null	Het
Skint1	T	A	4: 111,878,720 (GRCm39)	C217*	probably null	Het
Slc50a1	T	C	3: 89,176,460 (GRCm39)	Y82C	probably damaging	Het
Slc9a4	T	C	1: 40,651,423 (GRCm39)	V567A	probably benign	Het
Snx27	A	T	3: 94,410,270 (GRCm39)	W469R	probably damaging	Het
Sos2	A	G	12: 69,643,569 (GRCm39)	L937P	probably damaging	Het
Ssh1	T	C	5: 114,081,181 (GRCm39)	T728A	probably benign	Het
Tnfrsf8	G	A	4: 145,019,257 (GRCm39)	R193C	probably benign	Het
Tut4	T	C	4: 108,370,120 (GRCm39)	V673A	probably damaging	Het
Usp33	T	A	3: 152,085,113 (GRCm39)	M583K	possibly damaging	Het
Usp33	G	A	3: 152,085,233 (GRCm39)	C623Y	probably damaging	Het
Wdfy3	T	C	5: 102,017,855 (GRCm39)	I2562V	probably damaging	Het
Wnk2	T	C	13: 49,220,782 (GRCm39)	D1175G	probably damaging	Het
Zfp341	G	A	2: 154,474,209 (GRCm39)	E338K	probably damaging	Het
Zfp398	A	G	6: 47,817,638 (GRCm39)		probably benign	Het
Zp2	T	A	7: 119,732,562 (GRCm39)	K661N	probably null	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
R1806:Lhx1	UTSW	11	84,414,967 (GRCm39)	missense	probably damaging	1.00
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
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'- GCTGTTCTCTTTGGCGACAC -3'
(R):5'- GGGGCCTTAACTCTAACCGAATG -3'

Sequencing Primer
(F):5'- GACACTGCTGTTACTCAGGTAATC -3'
(R):5'- AACTCTAACCGAATGTATTTTCCTC -3'

Posted On

2017-02-10