Mutagenetix > Incidental Mutation

Incidental Mutation 'R1932:Lhx9'

215427

Institutional Source

Beutler Lab

Gene Symbol

Lhx9

Ensembl Gene

ENSMUSG00000019230

Gene Name

LIM homeobox protein 9

Synonyms

3110009O07Rik, Lhx9 alpha, LH2B

MMRRC Submission

039950-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.743) question?

Stock #

R1932 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

138825186-138848577 bp(-) (GRCm38)

Type of Mutation

start gained

DNA Base Change (assembly)

T to A at 138842009 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000142268 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000019374] [ENSMUST00000046870] [ENSMUST00000093486] [ENSMUST00000112026] [ENSMUST00000112030] [ENSMUST00000194557]

AlphaFold

Q9WUH2

Predicted Effect

probably benign
Transcript: ENSMUST00000019374

SMART Domains

Protein: ENSMUSP00000019374
Gene: ENSMUSG00000019230

Domain	Start	End	E-Value	Type
LIM	70	123	4.48e-17	SMART
LIM	132	186	8.04e-19	SMART
HOX	267	319	1.89e-4	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000046870

SMART Domains

Protein: ENSMUSP00000036480
Gene: ENSMUSG00000019230

Domain	Start	End	E-Value	Type
LIM	61	114	4.48e-17	SMART
LIM	123	177	8.04e-19	SMART
HOX	258	320	8.07e-22	SMART
low complexity region	344	368	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000093486

SMART Domains

Protein: ENSMUSP00000091198
Gene: ENSMUSG00000019230

Domain	Start	End	E-Value	Type
LIM	61	114	4.48e-17	SMART
LIM	123	177	8.04e-19	SMART
HOX	258	310	1.89e-4	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000112026

SMART Domains

Protein: ENSMUSP00000107657
Gene: ENSMUSG00000019230

Domain	Start	End	E-Value	Type
LIM	70	123	4.48e-17	SMART
LIM	132	186	8.04e-19	SMART
HOX	267	329	8.07e-22	SMART
low complexity region	353	377	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000112030

SMART Domains

Protein: ENSMUSP00000107661
Gene: ENSMUSG00000019230

Domain	Start	End	E-Value	Type
LIM	61	114	4.48e-17	SMART
LIM	123	177	8.04e-19	SMART
HOX	258	310	1.89e-4	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000194557

Coding Region Coverage

1x: 97.5%
3x: 97.0%
10x: 95.6%
20x: 93.3%

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 the LIM homeobox gene family of developmentally expressed transcription factors. The encoded protein contains a homeodomain and two cysteine-rich zinc-binding LIM domains involved in protein-protein interactions. The protein is highly similar to a mouse protein that causes gonadal agenesis when inactivated, suggesting a role in gonadal development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit failed proliferation of the somatic cells of the genital ridge resulting in lack of discrete gonad formation, infertility in both sexes, and female-like genitalia in genetically male mice. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcg4	T	A	9: 44,279,394 (GRCm38)	Q278H	probably benign	Het
Ace3	T	C	11: 106,004,610 (GRCm38)		probably null	Het
Aco1	T	C	4: 40,176,499 (GRCm38)	V221A	probably damaging	Het
Adamts20	T	A	15: 94,404,010 (GRCm38)	H27L	probably benign	Het
Adamts8	A	G	9: 30,956,512 (GRCm38)	D544G	probably benign	Het
Angptl4	C	A	17: 33,781,275 (GRCm38)	E40*	probably null	Het
Arsi	G	A	18: 60,916,651 (GRCm38)	G202E	probably benign	Het
Atf7ip2	T	A	16: 10,241,703 (GRCm38)	I369N	possibly damaging	Het
Atp6ap1l	T	A	13: 90,883,687 (GRCm38)	Y292F	probably damaging	Het
Atp6v1b2	A	T	8: 69,102,807 (GRCm38)	K217*	probably null	Het
Bid	C	T	6: 120,897,255 (GRCm38)	A110T	possibly damaging	Het
Blvra	T	A	2: 127,095,148 (GRCm38)	W174R	probably damaging	Het
Catsperg1	C	T	7: 29,198,143 (GRCm38)	G239R	probably damaging	Het
Ccdc157	G	T	11: 4,146,549 (GRCm38)	A400D	probably damaging	Het
Chd2	G	T	7: 73,454,445 (GRCm38)	P1298T	probably damaging	Het
CK137956	G	A	4: 127,946,858 (GRCm38)	L352F	possibly damaging	Het
Col22a1	G	A	15: 71,870,140 (GRCm38)	P503S	unknown	Het
Cox15	C	T	19: 43,746,785 (GRCm38)	R181H	probably benign	Het
Crem	C	T	18: 3,299,284 (GRCm38)	G47R	probably benign	Het
Crygs	T	A	16: 22,806,554 (GRCm38)	T46S	probably benign	Het
Cts8	T	A	13: 61,253,615 (GRCm38)	H62L	probably damaging	Het
Cyp4a32	T	A	4: 115,611,277 (GRCm38)	F319I	possibly damaging	Het
Dchs1	T	C	7: 105,765,902 (GRCm38)	S692G	probably damaging	Het
Ddx23	G	A	15: 98,650,718 (GRCm38)	R370W	possibly damaging	Het
Defa29	A	T	8: 21,326,849 (GRCm38)	S43T	probably damaging	Het
Dnajc14	A	G	10: 128,816,792 (GRCm38)	D573G	probably damaging	Het
Drd5	A	G	5: 38,319,976 (GRCm38)	Y104C	probably benign	Het
Efcab7	C	T	4: 99,911,018 (GRCm38)	P102L	probably damaging	Het
Efhc1	A	G	1: 20,967,400 (GRCm38)	Y267C	probably damaging	Het
Eif2ak4	T	C	2: 118,448,486 (GRCm38)	Y243H	probably damaging	Het
Gfm2	T	A	13: 97,141,967 (GRCm38)	I7N	probably damaging	Het
Gmds	A	G	13: 32,127,997 (GRCm38)	F150L	possibly damaging	Het
Gp2	T	C	7: 119,454,232 (GRCm38)	T169A	possibly damaging	Het
Grb14	A	G	2: 64,912,802 (GRCm38)	F508L	probably damaging	Het
Hdac5	T	A	11: 102,195,872 (GRCm38)		probably benign	Het
Heatr1	T	A	13: 12,435,185 (GRCm38)	M620K	probably damaging	Het
Herc3	A	G	6: 58,876,793 (GRCm38)	E608G	probably damaging	Het
Hoxb4	T	C	11: 96,320,041 (GRCm38)	Y156H	probably damaging	Het
Ifi205	T	A	1: 174,028,414 (GRCm38)	I17F	possibly damaging	Het
Il2rb	A	T	15: 78,491,777 (GRCm38)	S25T	possibly damaging	Het
Kansl1	T	C	11: 104,335,097 (GRCm38)	T998A	probably damaging	Het
Kcna6	G	T	6: 126,738,488 (GRCm38)	H479Q	probably benign	Het
Kif2a	T	C	13: 106,978,091 (GRCm38)	K350R	probably benign	Het
Lct	G	T	1: 128,294,161 (GRCm38)	A1547E	probably damaging	Het
Lingo1	T	A	9: 56,619,650 (GRCm38)	I552F	possibly damaging	Het
Lrp4	G	A	2: 91,497,355 (GRCm38)	W1516*	probably null	Het
Lrp5	C	T	19: 3,610,131 (GRCm38)	V978I	probably benign	Het
Ltbp1	T	A	17: 75,313,034 (GRCm38)	D719E	probably benign	Het
Ltbp4	A	G	7: 27,307,766 (GRCm38)		probably null	Het
Macf1	A	G	4: 123,452,037 (GRCm38)	I1326T	probably damaging	Het
Manba	T	C	3: 135,544,740 (GRCm38)	F376S	probably benign	Het
Mink1	T	C	11: 70,608,428 (GRCm38)		probably null	Het
Nfatc2ip	C	T	7: 126,384,992 (GRCm38)	V410I	probably damaging	Het
Nlrp1b	A	T	11: 71,182,138 (GRCm38)	I293N	probably damaging	Het
Olfr432	T	C	1: 174,050,678 (GRCm38)	Y102H	probably damaging	Het
Otol1	A	C	3: 70,028,104 (GRCm38)	E476D	probably benign	Het
Pcdhb4	C	T	18: 37,309,541 (GRCm38)	P635S	probably benign	Het
Pfkfb4	T	A	9: 108,999,169 (GRCm38)	F91I	probably damaging	Het
Polq	G	A	16: 37,062,304 (GRCm38)	R1610Q	possibly damaging	Het
Polr3c	A	T	3: 96,719,298 (GRCm38)	L270H	probably damaging	Het
Ppp1r15b	C	T	1: 133,131,625 (GRCm38)		probably benign	Het
Prkca	T	G	11: 108,192,149 (GRCm38)	D90A	probably benign	Het
Sall3	T	C	18: 80,969,753 (GRCm38)	D1156G	probably benign	Het
Scn7a	A	T	2: 66,676,102 (GRCm38)	L1481H	probably damaging	Het
Selenon	A	T	4: 134,544,618 (GRCm38)	I292N	probably damaging	Het
Sema6d	T	A	2: 124,659,886 (GRCm38)		probably null	Het
Sgpp1	G	T	12: 75,716,179 (GRCm38)	Y409*	probably null	Het
Sh3pxd2a	A	G	19: 47,267,508 (GRCm38)	S924P	probably benign	Het
Slc25a13	A	G	6: 6,042,264 (GRCm38)	V638A	probably benign	Het
Snhg11	T	C	2: 158,376,826 (GRCm38)		probably benign	Het
Sorbs2	A	G	8: 45,796,352 (GRCm38)	Q800R	probably benign	Het
Srf	C	A	17: 46,549,986 (GRCm38)	G401C	probably damaging	Het
Stradb	A	C	1: 58,991,105 (GRCm38)	N173H	probably benign	Het
Swap70	C	T	7: 110,279,263 (GRCm38)	A480V	possibly damaging	Het
Sycp2	A	G	2: 178,381,957 (GRCm38)	V422A	probably damaging	Het
Taf4	G	A	2: 179,932,029 (GRCm38)	T682M	probably damaging	Het
Tet3	T	C	6: 83,404,379 (GRCm38)	N269S	possibly damaging	Het
Thap12	A	T	7: 98,716,838 (GRCm38)	I738F	possibly damaging	Het
Tiam2	C	T	17: 3,514,725 (GRCm38)	R1413C	possibly damaging	Het
Tmem229a	A	T	6: 24,955,011 (GRCm38)	F248Y	probably damaging	Het
Tmprss7	G	A	16: 45,684,593 (GRCm38)	Q145*	probably null	Het
Tnc	A	T	4: 63,993,025 (GRCm38)		probably null	Het
Tonsl	A	T	15: 76,624,597 (GRCm38)	Y21N	probably damaging	Het
Tpr	A	G	1: 150,421,663 (GRCm38)	D1009G	probably benign	Het
Trpm2	G	A	10: 77,941,158 (GRCm38)	A435V	probably damaging	Het
Ubr3	T	A	2: 69,953,476 (GRCm38)		probably null	Het
Vcan	T	C	13: 89,705,534 (GRCm38)	N436D	possibly damaging	Het
Vmn2r104	T	A	17: 20,040,769 (GRCm38)	Y464F	probably damaging	Het
Vmn2r44	T	A	7: 8,367,982 (GRCm38)	R688S	probably benign	Het
Wdr74	G	T	19: 8,737,947 (GRCm38)	V157L	probably benign	Het
Wnt7a	T	A	6: 91,394,548 (GRCm38)	D144V	probably benign	Het
Zfp106	C	T	2: 120,531,681 (GRCm38)	A986T	possibly damaging	Het

Other mutations in Lhx9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00955:Lhx9	APN	1	138,828,680 (GRCm38)	missense	possibly damaging	0.74
IGL01624:Lhx9	APN	1	138,832,783 (GRCm38)	nonsense	probably null
IGL02149:Lhx9	APN	1	138,831,434 (GRCm38)	missense	probably damaging	1.00
IGL02452:Lhx9	APN	1	138,841,842 (GRCm38)	missense	probably damaging	1.00
IGL02982:Lhx9	APN	1	138,838,611 (GRCm38)	missense	probably damaging	1.00
R0123:Lhx9	UTSW	1	138,838,679 (GRCm38)	missense	probably damaging	1.00
R0134:Lhx9	UTSW	1	138,838,679 (GRCm38)	missense	probably damaging	1.00
R0141:Lhx9	UTSW	1	138,840,006 (GRCm38)	missense	possibly damaging	0.86
R0225:Lhx9	UTSW	1	138,838,679 (GRCm38)	missense	probably damaging	1.00
R0281:Lhx9	UTSW	1	138,832,904 (GRCm38)	missense	probably benign	0.00
R1460:Lhx9	UTSW	1	138,838,709 (GRCm38)	splice site	probably benign
R4738:Lhx9	UTSW	1	138,832,748 (GRCm38)	missense	probably damaging	1.00
R4792:Lhx9	UTSW	1	138,838,351 (GRCm38)	missense	possibly damaging	0.87
R4820:Lhx9	UTSW	1	138,838,367 (GRCm38)	missense	probably benign	0.00
R4877:Lhx9	UTSW	1	138,838,354 (GRCm38)	missense	probably benign	0.04
R6035:Lhx9	UTSW	1	138,838,543 (GRCm38)	missense	possibly damaging	0.67
R6035:Lhx9	UTSW	1	138,838,543 (GRCm38)	missense	possibly damaging	0.67
R6825:Lhx9	UTSW	1	138,841,806 (GRCm38)	frame shift	probably null
R6852:Lhx9	UTSW	1	138,841,806 (GRCm38)	frame shift	probably null
R6853:Lhx9	UTSW	1	138,841,806 (GRCm38)	frame shift	probably null
R7264:Lhx9	UTSW	1	138,832,751 (GRCm38)	missense	probably damaging	0.98
R8097:Lhx9	UTSW	1	138,838,351 (GRCm38)	missense	probably damaging	0.97
R8164:Lhx9	UTSW	1	138,832,780 (GRCm38)	missense	probably damaging	1.00
R8245:Lhx9	UTSW	1	138,838,441 (GRCm38)	missense	probably benign	0.24
R8278:Lhx9	UTSW	1	138,838,586 (GRCm38)	missense	probably damaging	0.98
R8951:Lhx9	UTSW	1	138,841,966 (GRCm38)	missense	probably damaging	1.00
R9761:Lhx9	UTSW	1	138,847,196 (GRCm38)	missense	probably benign	0.09
Z1177:Lhx9	UTSW	1	138,831,498 (GRCm38)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- TGAGTGCCTTTGGTCAGACG -3'
(R):5'- GCAGTTAGAATCGCCTGCTTTTC -3'

Sequencing Primer
(F):5'- TCAGACGGGCCTCAGTCTTG -3'
(R):5'- CCCTCTCAAGTAGAGCTATT -3'

Posted On

2014-07-14