Mutagenetix > Incidental Mutation

Incidental Mutation 'R0281:Lhx9'

37490

Institutional Source

Beutler Lab

Gene Symbol

Lhx9

Ensembl Gene

ENSMUSG00000019230

Gene Name

LIM homeobox protein 9

Synonyms

3110009O07Rik, Lhx9 alpha, LH2B

MMRRC Submission

038503-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.787) question?

Stock #

R0281 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

138752924-138776315 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 138760642 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Aspartic acid at position 236 (G236D)

Ref Sequence

ENSEMBL: ENSMUSP00000107661 (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: G245D

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000019374
Gene: ENSMUSG00000019230
AA Change: G245D

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: G236D

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000036480
Gene: ENSMUSG00000019230
AA Change: G236D

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: G236D

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000091198
Gene: ENSMUSG00000019230
AA Change: G236D

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: G245D

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000107657
Gene: ENSMUSG00000019230
AA Change: G245D

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: G236D

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000107661
Gene: ENSMUSG00000019230
AA Change: G236D

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

0.0733

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.7%
20x: 93.9%

Validation Efficiency

98% (104/106)

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: 101 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933430I17Rik	A	T	4: 62,464,304 (GRCm39)	R374*	probably null	Het
5930422O12Rik	A	T	8: 33,919,407 (GRCm39)	R76*	probably null	Het
A1cf	G	A	19: 31,923,214 (GRCm39)	A505T	probably benign	Het
Abcc5	T	A	16: 20,241,150 (GRCm39)	I12F	probably damaging	Het
Abcf2	T	C	5: 24,771,562 (GRCm39)	E555G	probably damaging	Het
Acan	A	T	7: 78,750,033 (GRCm39)	E1601D	probably damaging	Het
Acsbg3	T	A	17: 57,192,169 (GRCm39)	Y577*	probably null	Het
Adam2	T	A	14: 66,275,055 (GRCm39)	K559N	probably benign	Het
Akap11	A	C	14: 78,747,529 (GRCm39)	D1619E	possibly damaging	Het
Ankrd11	T	C	8: 123,622,307 (GRCm39)	D515G	probably benign	Het
Ankrd27	T	A	7: 35,318,796 (GRCm39)	N562K	probably damaging	Het
Atp10b	T	C	11: 43,044,131 (GRCm39)	I119T	probably benign	Het
Atr	T	C	9: 95,819,619 (GRCm39)	I2202T	probably benign	Het
Bltp2	C	T	11: 78,162,750 (GRCm39)	L871F	possibly damaging	Het
Brd4	T	A	17: 32,432,514 (GRCm39)		probably benign	Het
Catsperg2	C	T	7: 29,405,996 (GRCm39)	C634Y	possibly damaging	Het
Cep192	A	G	18: 67,961,553 (GRCm39)		probably benign	Het
Cfap65	T	A	1: 74,966,230 (GRCm39)	I366F	probably damaging	Het
Cnga4	G	T	7: 105,056,875 (GRCm39)	R326L	probably damaging	Het
Cntnap5b	T	A	1: 99,999,878 (GRCm39)	M212K	probably benign	Het
Col6a6	T	A	9: 105,661,315 (GRCm39)	M265L	probably benign	Het
Cspg4b	A	T	13: 113,505,677 (GRCm39)	I727F	probably damaging	Het
Cyp26b1	A	T	6: 84,551,538 (GRCm39)	F417Y	probably damaging	Het
Dhx15	A	T	5: 52,308,088 (GRCm39)	M768K	probably benign	Het
Drc7	G	A	8: 95,797,881 (GRCm39)	R433H	possibly damaging	Het
Duox2	C	T	2: 122,122,785 (GRCm39)	V550M	probably benign	Het
Elmo2	A	G	2: 165,138,810 (GRCm39)	L456P	probably damaging	Het
Fbxo39	T	C	11: 72,208,356 (GRCm39)	I236T	probably benign	Het
Fezf2	A	G	14: 12,343,977 (GRCm38)	C305R	probably damaging	Het
Fndc3b	C	A	3: 27,511,155 (GRCm39)	C785F	probably benign	Het
Gm12253	T	C	11: 58,330,838 (GRCm39)		probably benign	Het
Gnat2	T	A	3: 108,002,878 (GRCm39)	Y95*	probably null	Het
Gopc	T	C	10: 52,226,774 (GRCm39)	K220E	probably damaging	Het
Hectd4	G	A	5: 121,392,314 (GRCm39)	D193N	possibly damaging	Het
Hexa	G	A	9: 59,461,509 (GRCm39)		probably null	Het
Hspa4l	T	C	3: 40,739,840 (GRCm39)		probably benign	Het
Hspa5	T	C	2: 34,664,332 (GRCm39)	S301P	probably damaging	Het
Ice1	A	T	13: 70,752,166 (GRCm39)	S1307T	possibly damaging	Het
Igtp	T	C	11: 58,096,880 (GRCm39)	L17P	probably damaging	Het
Itk	T	C	11: 46,244,743 (GRCm39)	Y225C	probably damaging	Het
Kifc3	A	G	8: 95,830,088 (GRCm39)	V560A	probably damaging	Het
Lama1	A	G	17: 68,124,564 (GRCm39)	N2875D	probably damaging	Het
Lasp1	C	A	11: 97,697,677 (GRCm39)	C32*	probably null	Het
Lcp2	T	A	11: 34,019,854 (GRCm39)		probably benign	Het
Lrrc38	A	T	4: 143,076,979 (GRCm39)	I81F	probably damaging	Het
Ly6a	C	T	15: 74,867,236 (GRCm39)	V94M	probably benign	Het
Map3k13	A	G	16: 21,732,907 (GRCm39)	E503G	probably damaging	Het
Mertk	T	C	2: 128,624,541 (GRCm39)		probably benign	Het
Mrtfb	T	A	16: 13,230,027 (GRCm39)	I915N	probably damaging	Het
Msantd2	G	A	9: 37,434,515 (GRCm39)	D252N	possibly damaging	Het
Mtmr12	T	A	15: 12,257,792 (GRCm39)	L290*	probably null	Het
Myo3a	T	C	2: 22,250,409 (GRCm39)	I92T	probably benign	Het
Naglu	T	A	11: 100,964,853 (GRCm39)	N313K	probably damaging	Het
Nceh1	T	C	3: 27,276,953 (GRCm39)	V92A	possibly damaging	Het
Ncf4	A	G	15: 78,135,083 (GRCm39)	T47A	probably damaging	Het
Nrp1	T	A	8: 129,187,164 (GRCm39)	F403L	probably damaging	Het
Nxph3	T	C	11: 95,402,082 (GRCm39)	T111A	possibly damaging	Het
Obscn	T	A	11: 58,929,441 (GRCm39)	E6061V	probably damaging	Het
Obsl1	C	A	1: 75,469,571 (GRCm39)	G1149W	probably damaging	Het
Or14c39	A	G	7: 86,344,068 (GRCm39)	T135A	probably benign	Het
Or2k2	A	T	4: 58,784,981 (GRCm39)	V247E	probably damaging	Het
Or2p2	T	A	13: 21,256,544 (GRCm39)	Y309F	probably benign	Het
Or5b123	A	G	19: 13,596,849 (GRCm39)	T65A	probably benign	Het
Or5d14	C	T	2: 87,880,756 (GRCm39)	V71I	possibly damaging	Het
Or5p68	A	C	7: 107,946,121 (GRCm39)	D22E	probably benign	Het
Or6c70	T	A	10: 129,710,415 (GRCm39)	L70F	possibly damaging	Het
Pde9a	T	C	17: 31,674,080 (GRCm39)	V55A	probably damaging	Het
Pip4k2c	A	T	10: 127,041,690 (GRCm39)		probably null	Het
Plvap	T	C	8: 71,964,026 (GRCm39)	N112S	probably damaging	Het
Pop1	T	A	15: 34,530,004 (GRCm39)		probably null	Het
Ppip5k2	T	C	1: 97,644,278 (GRCm39)	H1113R	possibly damaging	Het
Ptprk	A	T	10: 28,449,388 (GRCm39)	I962F	probably damaging	Het
Rad51ap2	T	C	12: 11,507,043 (GRCm39)	S322P	possibly damaging	Het
Rasal1	A	G	5: 120,812,670 (GRCm39)	T565A	probably benign	Het
Rbm15	C	A	3: 107,238,471 (GRCm39)	R642S	probably damaging	Het
Rpsa	G	A	9: 119,960,069 (GRCm39)	E211K	possibly damaging	Het
Ryr3	A	G	2: 112,517,155 (GRCm39)	S3303P	probably damaging	Het
Scg2	T	A	1: 79,413,229 (GRCm39)	N458I	possibly damaging	Het
Setx	A	G	2: 29,069,655 (GRCm39)	T2487A	probably benign	Het
Slc4a5	G	A	6: 83,244,549 (GRCm39)		probably benign	Het
Slc8a2	T	A	7: 15,874,914 (GRCm39)	D387E	probably benign	Het
Smarcc2	A	G	10: 128,310,591 (GRCm39)	T407A	probably benign	Het
Snap25	A	G	2: 136,619,384 (GRCm39)	D179G	probably damaging	Het
Socs4	T	C	14: 47,527,325 (GRCm39)	S74P	probably benign	Het
Sp6	T	A	11: 96,912,751 (GRCm39)	Y155N	probably benign	Het
Srrt	C	T	5: 137,294,389 (GRCm39)		probably benign	Het
Steap1	C	T	5: 5,786,431 (GRCm39)	M335I	probably benign	Het
Stra6	A	T	9: 58,052,772 (GRCm39)	Y250F	probably benign	Het
Svil	T	C	18: 5,094,582 (GRCm39)	S1421P	probably damaging	Het
Tcea3	G	A	4: 135,998,677 (GRCm39)	C317Y	probably damaging	Het
Tmco6	T	C	18: 36,870,757 (GRCm39)	L117S	probably damaging	Het
Trp53bp1	T	C	2: 121,100,718 (GRCm39)	K89E	probably damaging	Het
Trp63	T	A	16: 25,583,052 (GRCm39)		probably benign	Het
Ube2d2a	A	G	18: 35,933,185 (GRCm39)	Y74C	probably damaging	Het
Usp19	T	G	9: 108,375,708 (GRCm39)	F885V	probably damaging	Het
Utp18	T	A	11: 93,773,003 (GRCm39)		probably benign	Het
Vmn2r116	T	C	17: 23,620,387 (GRCm39)	I707T	possibly damaging	Het
Vmn2r68	T	A	7: 84,882,457 (GRCm39)		probably benign	Het
Vmn2r68	C	G	7: 84,882,466 (GRCm39)		probably null	Het
Zfp318	C	T	17: 46,723,540 (GRCm39)	P1848S	probably benign	Het
Zfp984	G	T	4: 147,839,722 (GRCm39)	N376K	probably benign	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
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
R4820:Lhx9	UTSW	1	138,766,105 (GRCm39)	missense	probably benign	0.00
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'- AGCCAATGACGGATGTGGCTTAC -3'
(R):5'- GTGTCCAGGTCTCCCATGTTAGTTG -3'

Sequencing Primer
(F):5'- CGGATGTGGCTTACCTGTAAAAC -3'
(R):5'- GTTGACTGTAGCCACTGTCTTC -3'

Posted On

2013-05-23