Mutagenetix > Incidental Mutation

Incidental Mutation 'R4820:Lhx9'

370090

Institutional Source

Beutler Lab

Gene Symbol

Lhx9

Ensembl Gene

ENSMUSG00000019230

Gene Name

LIM homeobox protein 9

Synonyms

3110009O07Rik, Lhx9 alpha, LH2B

MMRRC Submission

042436-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.787) question?

Stock #

R4820 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

138752924-138776315 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 138766105 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Leucine at position 237 (V237L)

Ref Sequence

ENSEMBL: ENSMUSP00000107657 (fasta)

Gene Model

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

AlphaFold

Q9WUH2

Predicted Effect

probably benign
Transcript: ENSMUST00000019374
AA Change: V237L

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

SMART Domains

Protein: ENSMUSP00000019374
Gene: ENSMUSG00000019230
AA Change: V237L

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
AA Change: V228L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000036480
Gene: ENSMUSG00000019230
AA Change: V228L

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
AA Change: V228L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000091198
Gene: ENSMUSG00000019230
AA Change: V228L

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
AA Change: V237L

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

SMART Domains

Protein: ENSMUSP00000107657
Gene: ENSMUSG00000019230
AA Change: V237L

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
AA Change: V228L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000107661
Gene: ENSMUSG00000019230
AA Change: V228L

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

noncoding transcript
Transcript: ENSMUST00000192425

Predicted Effect

probably benign
Transcript: ENSMUST00000194557

Meta Mutation Damage Score

0.0834

Coding Region Coverage

1x: 99.0%
3x: 98.3%
10x: 96.5%
20x: 92.9%

Validation Efficiency

96% (104/108)

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: 95 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930488N24Rik	T	C	17: 14,326,481 (GRCm39)		noncoding transcript	Het
5730455P16Rik	A	T	11: 80,266,346 (GRCm39)	S132T	possibly damaging	Het
Aadacl3	T	A	4: 144,184,527 (GRCm39)	H77L	probably damaging	Het
Actr5	T	A	2: 158,467,426 (GRCm39)	V122D	probably damaging	Het
Adamts7	A	G	9: 90,071,739 (GRCm39)	D678G	possibly damaging	Het
Alpk1	T	A	3: 127,464,708 (GRCm39)	D1190V	probably benign	Het
Apbb1ip	A	T	2: 22,765,265 (GRCm39)	N649Y	unknown	Het
Atp6v0a1	A	G	11: 100,933,776 (GRCm39)	I522V	probably benign	Het
Brd10	T	C	19: 29,695,809 (GRCm39)	N1228S	possibly damaging	Het
Cars1	T	C	7: 143,124,301 (GRCm39)	D375G	probably damaging	Het
Catspere1	A	T	1: 177,687,441 (GRCm39)		noncoding transcript	Het
Ccdc87	A	G	19: 4,890,579 (GRCm39)	D357G	probably damaging	Het
Cd101	A	T	3: 100,929,471 (GRCm39)	S8T	probably benign	Het
Cfap65	C	T	1: 74,966,791 (GRCm39)	A299T	probably benign	Het
Cic	T	C	7: 24,971,157 (GRCm39)	V296A	possibly damaging	Het
Col7a1	T	A	9: 108,797,675 (GRCm39)	S1686T	possibly damaging	Het
Ctbp2	A	C	7: 132,615,423 (GRCm39)	L504R	probably damaging	Het
Cttnbp2nl	T	C	3: 104,918,640 (GRCm39)	K67E	probably benign	Het
Cyp2c50	C	T	19: 40,102,024 (GRCm39)	P480S	probably damaging	Het
Dcdc5	A	C	2: 106,166,420 (GRCm39)		noncoding transcript	Het
Defb2	G	T	8: 22,333,317 (GRCm39)	E31*	probably null	Het
Dhrs1	T	A	14: 55,977,083 (GRCm39)	N244I	possibly damaging	Het
Dop1b	A	G	16: 93,589,978 (GRCm39)	I134V	probably benign	Het
Eif1ad11	A	T	12: 87,994,158 (GRCm39)	I129F	unknown	Het
Etl4	A	G	2: 20,811,496 (GRCm39)	D1193G	possibly damaging	Het
Ezh1	A	C	11: 101,094,594 (GRCm39)	S399R	probably damaging	Het
Fam161a	T	C	11: 22,970,076 (GRCm39)	S26P	probably damaging	Het
Fcgbp	C	A	7: 27,813,383 (GRCm39)	S2306Y	probably damaging	Het
Fras1	T	C	5: 96,876,512 (GRCm39)	I2415T	probably benign	Het
Gas2l3	A	G	10: 89,252,907 (GRCm39)	L246P	probably damaging	Het
Gdf15	C	T	8: 71,082,246 (GRCm39)	V287M	probably damaging	Het
Gm7742	T	C	17: 21,420,235 (GRCm39)		noncoding transcript	Het
Grin2d	T	C	7: 45,507,363 (GRCm39)	D446G	probably damaging	Het
Hemk1	A	G	9: 107,205,385 (GRCm39)	F107L	probably benign	Het
Hmgcr	C	T	13: 96,796,700 (GRCm39)	G197S	probably damaging	Het
Ift52	G	A	2: 162,873,108 (GRCm39)	G207D	probably benign	Het
Il17re	A	G	6: 113,442,816 (GRCm39)	T275A	probably benign	Het
Iqcf3	T	C	9: 106,430,788 (GRCm39)		probably benign	Het
Kcna1	A	G	6: 126,619,099 (GRCm39)	I407T	probably damaging	Het
Kcnrg	T	A	14: 61,845,386 (GRCm39)	M142K	probably benign	Het
Lipo3	A	C	19: 33,560,497 (GRCm39)	I56S	probably damaging	Het
Loxhd1	C	G	18: 77,472,663 (GRCm39)	P1060R	probably damaging	Het
Map2k4	A	C	11: 65,587,201 (GRCm39)		probably benign	Het
Methig1	A	G	15: 100,251,416 (GRCm39)	K109R	possibly damaging	Het
Mmrn1	G	A	6: 60,950,027 (GRCm39)	V326I	probably benign	Het
Myo15a	G	A	11: 60,367,741 (GRCm39)	R167H	probably damaging	Het
Ncoa7	G	A	10: 30,524,472 (GRCm39)	T142M	probably damaging	Het
Nfkb2	C	A	19: 46,296,493 (GRCm39)	Q254K	probably damaging	Het
Nherf1	A	G	11: 115,070,918 (GRCm39)	E290G	probably benign	Het
Nol6	G	T	4: 41,121,508 (GRCm39)	P278Q	probably damaging	Het
Nptxr	T	A	15: 79,677,027 (GRCm39)	D285V	probably damaging	Het
Oosp3	T	C	19: 11,688,997 (GRCm39)	W82R	probably damaging	Het
Or6b3	A	T	1: 92,438,812 (GRCm39)	*313K	probably null	Het
Or6n1	A	G	1: 173,916,742 (GRCm39)	I45M	possibly damaging	Het
Pa2g4	G	T	10: 128,395,199 (GRCm39)	T322K	probably damaging	Het
Parp16	C	A	9: 65,145,175 (GRCm39)	F291L	probably damaging	Het
Pdzd9	A	T	7: 120,267,619 (GRCm39)	D65E	probably damaging	Het
Pgap3	A	G	11: 98,281,300 (GRCm39)	W238R	probably damaging	Het
Pgf	G	A	12: 85,218,538 (GRCm39)	H67Y	probably benign	Het
Pik3cb	T	C	9: 98,955,679 (GRCm39)	T413A	probably benign	Het
Plcxd2	A	T	16: 45,800,700 (GRCm39)	C175S	probably benign	Het
Pou2f1	A	T	1: 165,719,517 (GRCm39)		probably benign	Het
Ppfia1	T	G	7: 144,052,106 (GRCm39)	N846T	probably benign	Het
Ppid	T	A	3: 79,502,504 (GRCm39)		probably null	Het
Prkcq	G	A	2: 11,231,797 (GRCm39)		probably null	Het
Ptgds	T	C	2: 25,359,058 (GRCm39)	K66E	probably benign	Het
Ptpmt1	A	G	2: 90,748,283 (GRCm39)		noncoding transcript	Het
Rab3il1	G	A	19: 10,004,034 (GRCm39)	G51D	probably benign	Het
Rdx	T	C	9: 51,974,891 (GRCm39)	V9A	probably damaging	Het
Rpl7l1	T	C	17: 47,089,014 (GRCm39)	N239S	probably benign	Het
Rrbp1	C	A	2: 143,806,685 (GRCm39)	A978S	possibly damaging	Het
Rsf1	GCGGCGGCG	GCGGCGGCGCCGGCGGCG	7: 97,229,126 (GRCm39)		probably benign	Het
Scn3a	A	T	2: 65,291,622 (GRCm39)	I1708N	probably damaging	Het
Serinc1	A	G	10: 57,401,466 (GRCm39)	I109T	possibly damaging	Het
Shroom1	G	A	11: 53,355,966 (GRCm39)	V339I	probably benign	Het
Slc30a8	T	A	15: 52,169,880 (GRCm39)	C36S	probably benign	Het
Slco1b2	A	G	6: 141,631,158 (GRCm39)	I597M	probably benign	Het
Snx27	A	G	3: 94,427,518 (GRCm39)	F228S	probably damaging	Het
Spata31f1a	T	A	4: 42,851,815 (GRCm39)	I114F	probably damaging	Het
Speer4e2	G	T	5: 15,026,225 (GRCm39)	T144K	probably benign	Het
Stim1	T	A	7: 102,064,571 (GRCm39)	F214I	probably damaging	Het
Svep1	T	C	4: 58,082,664 (GRCm39)	T1987A	probably benign	Het
Tamm41	A	G	6: 115,002,378 (GRCm39)	I18T	possibly damaging	Het
Tmem150b	T	A	7: 4,726,871 (GRCm39)	D79V	probably damaging	Het
Tmem167	T	A	13: 90,252,548 (GRCm39)	I68N	probably benign	Het
Traf3	A	G	12: 111,227,204 (GRCm39)	E339G	possibly damaging	Het
Tspan12	G	A	6: 21,795,660 (GRCm39)	P177S	probably damaging	Het
Ttn	A	G	2: 76,783,562 (GRCm39)	I810T	probably benign	Het
Ulk1	T	C	5: 110,939,996 (GRCm39)	T407A	probably benign	Het
Uroc1	G	A	6: 90,334,600 (GRCm39)		probably null	Het
Vmn2r-ps69	T	C	7: 84,959,584 (GRCm39)		noncoding transcript	Het
Wdr59	T	C	8: 112,207,446 (GRCm39)	N476S	probably benign	Het
Zfp472	A	G	17: 33,196,416 (GRCm39)	M164V	probably benign	Het
Zfp608	T	C	18: 55,120,756 (GRCm39)	N277S	probably benign	Het
Zfp831	T	C	2: 174,547,097 (GRCm39)	C1427R	possibly damaging	Het

Other mutations in Lhx9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00955:Lhx9	APN	1	138,756,418 (GRCm39)	missense	possibly damaging	0.74
IGL01624:Lhx9	APN	1	138,760,521 (GRCm39)	nonsense	probably null
IGL02149:Lhx9	APN	1	138,759,172 (GRCm39)	missense	probably damaging	1.00
IGL02452:Lhx9	APN	1	138,769,580 (GRCm39)	missense	probably damaging	1.00
IGL02982:Lhx9	APN	1	138,766,349 (GRCm39)	missense	probably damaging	1.00
R0123:Lhx9	UTSW	1	138,766,417 (GRCm39)	missense	probably damaging	1.00
R0134:Lhx9	UTSW	1	138,766,417 (GRCm39)	missense	probably damaging	1.00
R0141:Lhx9	UTSW	1	138,767,744 (GRCm39)	missense	possibly damaging	0.86
R0225:Lhx9	UTSW	1	138,766,417 (GRCm39)	missense	probably damaging	1.00
R0281:Lhx9	UTSW	1	138,760,642 (GRCm39)	missense	probably benign	0.00
R1460:Lhx9	UTSW	1	138,766,447 (GRCm39)	splice site	probably benign
R1932:Lhx9	UTSW	1	138,769,747 (GRCm39)	start gained	probably benign
R4738:Lhx9	UTSW	1	138,760,486 (GRCm39)	missense	probably damaging	1.00
R4792:Lhx9	UTSW	1	138,766,089 (GRCm39)	missense	possibly damaging	0.87
R4877:Lhx9	UTSW	1	138,766,092 (GRCm39)	missense	probably benign	0.04
R6035:Lhx9	UTSW	1	138,766,281 (GRCm39)	missense	possibly damaging	0.67
R6035:Lhx9	UTSW	1	138,766,281 (GRCm39)	missense	possibly damaging	0.67
R6825:Lhx9	UTSW	1	138,769,544 (GRCm39)	frame shift	probably null
R6852:Lhx9	UTSW	1	138,769,544 (GRCm39)	frame shift	probably null
R6853:Lhx9	UTSW	1	138,769,544 (GRCm39)	frame shift	probably null
R7264:Lhx9	UTSW	1	138,760,489 (GRCm39)	missense	probably damaging	0.98
R8097:Lhx9	UTSW	1	138,766,089 (GRCm39)	missense	probably damaging	0.97
R8164:Lhx9	UTSW	1	138,760,518 (GRCm39)	missense	probably damaging	1.00
R8245:Lhx9	UTSW	1	138,766,179 (GRCm39)	missense	probably benign	0.24
R8278:Lhx9	UTSW	1	138,766,324 (GRCm39)	missense	probably damaging	0.98
R8951:Lhx9	UTSW	1	138,769,704 (GRCm39)	missense	probably damaging	1.00
R9761:Lhx9	UTSW	1	138,774,934 (GRCm39)	missense	probably benign	0.09
Z1177:Lhx9	UTSW	1	138,759,236 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- ATGGGCAACAAGGATTTGGC -3'
(R):5'- AAGGACAGCCTGGTGTACTG -3'

Sequencing Primer
(F):5'- GCAACAAGGATTTGGCTTTGC -3'
(R):5'- GTACTGCCGCGCACACTTC -3'

Posted On

2016-02-04