Mutagenetix > Incidental Mutation

Incidental Mutation 'R1565:Lhx1'

175212

Institutional Source

Beutler Lab

Gene Symbol

Lhx1

Ensembl Gene

ENSMUSG00000018698

Gene Name

LIM homeobox protein 1

Synonyms

Lim1

MMRRC Submission

039604-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1565 (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 84410647 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 226 (S226T)

Ref Sequence

ENSEMBL: ENSMUSP00000138899 (fasta)

Gene Model

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

AlphaFold

P63006

Predicted Effect

probably benign
Transcript: ENSMUST00000018842
AA Change: S317T

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000018842
Gene: ENSMUSG00000018698
AA Change: S317T

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: 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
AA Change: S226T

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000138899
Gene: ENSMUSG00000018698
AA Change: S226T

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

0.0595

Coding Region Coverage

1x: 99.0%
3x: 98.1%
10x: 95.5%
20x: 90.0%

Validation Efficiency

96% (82/85)

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: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2810021J22Rik	G	A	11: 58,771,327 (GRCm39)	G270S	probably benign	Het
Abtb1	T	C	6: 88,813,536 (GRCm39)	T401A	probably benign	Het
Adamts14	A	T	10: 61,106,676 (GRCm39)	M148K	probably damaging	Het
Adcy5	A	G	16: 35,089,327 (GRCm39)	E508G	probably damaging	Het
Ankfy1	T	A	11: 72,648,144 (GRCm39)	L875H	probably damaging	Het
Cacng3	A	T	7: 122,367,624 (GRCm39)	D168V	probably damaging	Het
Clpb	G	A	7: 101,434,668 (GRCm39)	R488Q	probably benign	Het
Cltrn	A	G	X: 162,901,230 (GRCm39)	D184G	possibly damaging	Het
Cpxm2	A	T	7: 131,663,874 (GRCm39)	Y350N	probably damaging	Het
D130040H23Rik	T	A	8: 69,755,812 (GRCm39)	*406R	probably null	Het
Dnah10	T	A	5: 124,906,678 (GRCm39)	D4236E	probably damaging	Het
Dpf3	T	A	12: 83,417,391 (GRCm39)	Y27F	probably damaging	Het
Esp4	T	C	17: 40,913,486 (GRCm39)	*118Q	probably null	Het
Fam222b	T	C	11: 78,045,488 (GRCm39)	S222P	possibly damaging	Het
Flnc	T	C	6: 29,455,170 (GRCm39)	V1933A	probably damaging	Het
Gem	T	C	4: 11,713,709 (GRCm39)	F282L	possibly damaging	Het
Gli2	T	C	1: 118,769,660 (GRCm39)	T631A	possibly damaging	Het
Gpld1	T	A	13: 25,140,051 (GRCm39)	V116E	probably damaging	Het
Gpr176	A	G	2: 118,110,695 (GRCm39)	M188T	probably benign	Het
Grk5	T	C	19: 61,078,410 (GRCm39)	V489A	probably damaging	Het
Hpdl	T	C	4: 116,678,080 (GRCm39)	N127S	probably damaging	Het
Hsd17b8	C	T	17: 34,246,469 (GRCm39)	V105I	possibly damaging	Het
Id4	G	T	13: 48,415,770 (GRCm39)	V151L	possibly damaging	Het
Kcnh8	G	T	17: 53,263,909 (GRCm39)	G802V	probably benign	Het
Lamc1	C	A	1: 153,118,489 (GRCm39)	S894I	probably benign	Het
Larp1b	A	G	3: 40,926,819 (GRCm39)	N184S	probably damaging	Het
Lmo7	A	T	14: 102,124,957 (GRCm39)	Q472L	probably damaging	Het
Mog	G	C	17: 37,328,474 (GRCm39)	N152K	possibly damaging	Het
Mttp	A	G	3: 137,822,166 (GRCm39)		probably null	Het
Mycbp2	A	G	14: 103,489,945 (GRCm39)	V953A	possibly damaging	Het
Myo3a	A	T	2: 22,345,091 (GRCm39)	Y509F	probably damaging	Het
Myo9b	A	G	8: 71,767,836 (GRCm39)	N303S	possibly damaging	Het
Nek3	T	C	8: 22,622,217 (GRCm39)		probably null	Het
Nlrc4	A	T	17: 74,748,926 (GRCm39)	D771E	probably benign	Het
Nup160	A	T	2: 90,552,405 (GRCm39)	N1127I	possibly damaging	Het
Oas1h	A	T	5: 121,000,663 (GRCm39)	N91I	probably damaging	Het
Or13p4	T	A	4: 118,547,389 (GRCm39)	N87Y	probably damaging	Het
Or4c120	A	T	2: 89,000,971 (GRCm39)	V195D	probably benign	Het
Or4c121	G	T	2: 89,024,227 (GRCm39)	S50R	probably damaging	Het
Parp4	T	C	14: 56,827,329 (GRCm39)		probably benign	Het
Pi4ka	G	A	16: 17,099,764 (GRCm39)	C96Y	probably null	Het
Pira2	A	T	7: 3,847,548 (GRCm39)	F47Y	probably damaging	Het
Pkhd1	C	A	1: 20,417,681 (GRCm39)	G2490V	probably damaging	Het
Plekhg1	C	T	10: 3,890,526 (GRCm39)	T394I	probably damaging	Het
Pramel22	G	A	4: 143,382,187 (GRCm39)	Q170*	probably null	Het
Psmd1	T	C	1: 86,019,719 (GRCm39)		probably benign	Het
Rab3ip	A	T	10: 116,775,128 (GRCm39)	C77S	probably benign	Het
Reln	A	T	5: 22,130,211 (GRCm39)	M2700K	probably benign	Het
Rfx1	A	G	8: 84,800,575 (GRCm39)	T59A	probably benign	Het
Ric8b	G	T	10: 84,815,963 (GRCm39)	V405L	probably benign	Het
Rufy3	G	T	5: 88,788,491 (GRCm39)	A479S	probably damaging	Het
Sardh	A	T	2: 27,132,731 (GRCm39)	Y166N	probably damaging	Het
Slamf6	T	G	1: 171,761,975 (GRCm39)	V132G	possibly damaging	Het
Slc12a3	T	G	8: 95,072,505 (GRCm39)	H674Q	possibly damaging	Het
Sned1	G	A	1: 93,209,376 (GRCm39)	V830M	possibly damaging	Het
Srsf9	A	G	5: 115,465,429 (GRCm39)	N21S	possibly damaging	Het
Stkld1	A	T	2: 26,840,102 (GRCm39)	T391S	probably benign	Het
Sumf2	C	A	5: 129,888,755 (GRCm39)	N230K	probably damaging	Het
Tbc1d22a	T	C	15: 86,119,770 (GRCm39)	V22A	possibly damaging	Het
Thsd7b	T	A	1: 129,523,778 (GRCm39)	S194T	possibly damaging	Het
Tnn	T	A	1: 159,924,835 (GRCm39)	Y1173F	probably damaging	Het
Top2a	A	G	11: 98,891,880 (GRCm39)	F1122L	probably damaging	Het
Trappc9	G	A	15: 72,897,816 (GRCm39)	R377W	probably damaging	Het
Trim39	G	A	17: 36,579,746 (GRCm39)	R70W	probably damaging	Het
Ttn	G	A	2: 76,624,605 (GRCm39)	T15289I	probably damaging	Het
Ugt2b38	A	T	5: 87,559,773 (GRCm39)	V373E	probably damaging	Het
Usp54	A	G	14: 20,657,227 (GRCm39)	S24P	probably damaging	Het
Vmn2r27	C	T	6: 124,208,593 (GRCm39)	G51S	probably benign	Het
Xylt2	C	T	11: 94,558,420 (GRCm39)	A579T	probably benign	Het
Zbtb21	A	G	16: 97,753,627 (GRCm39)	S247P	probably benign	Het
Zc3h7b	C	T	15: 81,661,289 (GRCm39)	P376L	probably benign	Het
Zfp251	T	A	15: 76,737,238 (GRCm39)	R613S	probably damaging	Het
Zfp251	C	T	15: 76,737,239 (GRCm39)	R613K	possibly damaging	Het
Zfp91	T	C	19: 12,756,439 (GRCm39)	D135G	probably benign	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
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
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'- CCACCATTGACCGACAGAGATGAG -3'
(R):5'- GTTTTGTGCCAAGTGTCCAGCC -3'

Sequencing Primer
(F):5'- TGAGAAAGGTGGACTGGGC -3'
(R):5'- GGCAAGCCTGCTTTTGTAAC -3'

Posted On

2014-04-24