Mutagenetix > Incidental Mutation

Incidental Mutation 'R4792:Lhx9'

368642

Institutional Source

Beutler Lab

Gene Symbol

Lhx9

Ensembl Gene

ENSMUSG00000019230

Gene Name

LIM homeobox protein 9

Synonyms

3110009O07Rik, Lhx9 alpha, LH2B

MMRRC Submission

042419-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.787) question?

Stock #

R4792 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

138752924-138776315 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 138766089 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Phenylalanine at position 233 (Y233F)

Ref Sequence

ENSEMBL: ENSMUSP00000036480 (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: Y242F

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)

SMART Domains

Protein: ENSMUSP00000019374
Gene: ENSMUSG00000019230
AA Change: Y242F

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

possibly damaging
Transcript: ENSMUST00000046870
AA Change: Y233F

PolyPhen 2 Score 0.872 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000036480
Gene: ENSMUSG00000019230
AA Change: Y233F

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: Y233F

PolyPhen 2 Score 0.327 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000091198
Gene: ENSMUSG00000019230
AA Change: Y233F

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: Y242F

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)

SMART Domains

Protein: ENSMUSP00000107657
Gene: ENSMUSG00000019230
AA Change: Y242F

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: Y233F

PolyPhen 2 Score 0.327 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000107661
Gene: ENSMUSG00000019230
AA Change: Y233F

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

0.0708

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.6%
20x: 93.3%

Validation Efficiency

97% (89/92)

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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310061N02Rik	A	G	16: 88,504,651 (GRCm39)	S49P	possibly damaging	Het
Abcb1a	T	C	5: 8,796,657 (GRCm39)		probably null	Het
Adgb	G	A	10: 10,274,647 (GRCm39)	T770I	probably damaging	Het
Adgre4	A	T	17: 56,098,491 (GRCm39)	T134S	probably benign	Het
Aldh1a1	A	G	19: 20,597,349 (GRCm39)	N110S	probably damaging	Het
Alox5	C	A	6: 116,437,964 (GRCm39)	V8L	possibly damaging	Het
Ambra1	A	G	2: 91,603,191 (GRCm39)	T392A	possibly damaging	Het
Apob	A	G	12: 8,058,051 (GRCm39)	I2145V	probably benign	Het
Arhgap39	A	G	15: 76,625,717 (GRCm39)	Y196H	possibly damaging	Het
Armh2	A	G	13: 24,930,490 (GRCm39)		probably benign	Het
Carmil1	A	G	13: 24,251,173 (GRCm39)	L439S	probably damaging	Het
Carmil1	A	T	13: 24,325,659 (GRCm39)	S224T	possibly damaging	Het
Cfh	G	A	1: 140,028,561 (GRCm39)	Q706*	probably null	Het
Chd2	A	C	7: 73,118,325 (GRCm39)	S1098A	probably benign	Het
Chrna5	A	T	9: 54,911,985 (GRCm39)	I158F	probably damaging	Het
Cilk1	A	G	9: 78,060,975 (GRCm39)	D207G	probably damaging	Het
Col6a5	T	C	9: 105,807,983 (GRCm39)	T1022A	unknown	Het
Cul7	T	A	17: 46,967,976 (GRCm39)	Y423*	probably null	Het
Cyp2e1	T	C	7: 140,353,588 (GRCm39)	Y342H	probably benign	Het
D630045J12Rik	T	C	6: 38,125,275 (GRCm39)	K1580E	probably damaging	Het
Dnah6	A	G	6: 73,066,651 (GRCm39)	M2573T	probably damaging	Het
Dnai4	T	C	4: 102,929,881 (GRCm39)	K370R	possibly damaging	Het
Edem1	T	A	6: 108,805,707 (GRCm39)		probably benign	Het
Erp29	C	T	5: 121,585,237 (GRCm39)	E86K	probably benign	Het
Esrp2	C	A	8: 106,859,141 (GRCm39)	R535L	probably damaging	Het
Gabrb2	C	T	11: 42,420,330 (GRCm39)		probably benign	Het
Gpat3	C	T	5: 101,005,039 (GRCm39)	P58L	probably benign	Het
Herc1	T	A	9: 66,403,266 (GRCm39)	V4395E	possibly damaging	Het
Hivep2	C	A	10: 14,004,713 (GRCm39)	T437K	probably benign	Het
Hmgb2	G	A	8: 57,966,344 (GRCm39)	C106Y	probably damaging	Het
Hoxa10	T	C	6: 52,209,481 (GRCm39)		probably benign	Het
Hsd3b1	T	A	3: 98,760,226 (GRCm39)	Y255F	probably benign	Het
Ighd	T	C	12: 113,379,819 (GRCm39)	K42E	probably benign	Het
Ighv1-26	T	C	12: 114,752,191 (GRCm39)	Y51C	possibly damaging	Het
Ighv5-2	C	T	12: 113,542,419 (GRCm39)	E19K	possibly damaging	Het
Ipo11	T	C	13: 106,970,668 (GRCm39)		probably benign	Het
Itk	C	T	11: 46,235,658 (GRCm39)		probably benign	Het
Kat6a	T	A	8: 23,430,592 (GRCm39)	H1982Q	unknown	Het
Kdm4d	C	T	9: 14,374,686 (GRCm39)	V391I	probably benign	Het
Klk14	G	A	7: 43,341,501 (GRCm39)	C51Y	probably damaging	Het
Lgr6	T	A	1: 134,949,544 (GRCm39)	S229C	probably benign	Het
Lmf1	G	A	17: 25,873,445 (GRCm39)	V317M	probably damaging	Het
Mapk4	T	C	18: 74,070,321 (GRCm39)	T191A	probably damaging	Het
Mrc2	G	A	11: 105,239,257 (GRCm39)		probably null	Het
Naglu	C	T	11: 100,961,932 (GRCm39)	T135M	probably damaging	Het
Nomo1	T	A	7: 45,693,643 (GRCm39)		probably null	Het
Nop56	T	A	2: 130,119,784 (GRCm39)	V75E	possibly damaging	Het
Nr1i3	G	A	1: 171,046,164 (GRCm39)	C283Y	probably damaging	Het
Or4x6	T	A	2: 89,949,174 (GRCm39)	Y256F	possibly damaging	Het
Or51d1	G	A	7: 102,347,933 (GRCm39)	G163R	probably damaging	Het
Or6c38	T	G	10: 128,929,489 (GRCm39)	Y118S	probably damaging	Het
Pcdhga2	A	G	18: 37,802,452 (GRCm39)	S99G	probably benign	Het
Pcnx1	T	A	12: 81,965,925 (GRCm39)	D697E	probably damaging	Het
Plxnb1	G	A	9: 108,939,716 (GRCm39)	D1462N	probably damaging	Het
Pnn	G	T	12: 59,118,991 (GRCm39)	V525F	possibly damaging	Het
Prrc2a	A	T	17: 35,375,463 (GRCm39)	D1062E	probably damaging	Het
Prss35	T	A	9: 86,637,722 (GRCm39)	V164E	probably damaging	Het
Psapl1	T	C	5: 36,362,547 (GRCm39)	S380P	probably benign	Het
Rnf222	A	T	11: 68,783,845 (GRCm39)	E137D	probably damaging	Het
Rsph10b	A	G	5: 143,874,135 (GRCm39)	T79A	probably damaging	Het
Sbf2	T	C	7: 109,950,817 (GRCm39)	Q1164R	probably damaging	Het
Scn7a	T	C	2: 66,556,592 (GRCm39)	D331G	probably damaging	Het
Shtn1	G	C	19: 59,039,305 (GRCm39)	R45G	probably damaging	Het
Sspo	G	A	6: 48,438,519 (GRCm39)	S1529N	probably benign	Het
St8sia3	T	A	18: 64,398,634 (GRCm39)	V31E	probably benign	Het
Sult1b1	A	T	5: 87,662,906 (GRCm39)	W265R	probably damaging	Het
Supt5	G	T	7: 28,015,754 (GRCm39)	Q863K	probably benign	Het
Tbc1d31	A	G	15: 57,804,124 (GRCm39)	R380G	probably benign	Het
Tdpoz1	T	A	3: 93,577,845 (GRCm39)	D313V	possibly damaging	Het
Tmem260	CAGGGACCGGCATAG	CAG	14: 48,749,451 (GRCm39)		probably benign	Het
Tpx2	A	T	2: 152,727,016 (GRCm39)	T428S	probably damaging	Het
Trip11	A	T	12: 101,851,705 (GRCm39)	H786Q	probably benign	Het
Trpc6	A	T	9: 8,626,615 (GRCm39)	M322L	probably benign	Het
Try10	T	C	6: 41,332,386 (GRCm39)	V14A	probably benign	Het
Unc13d	A	T	11: 115,961,108 (GRCm39)	F416L	probably damaging	Het
Vmn2r75	A	T	7: 85,812,378 (GRCm39)	M547K	possibly damaging	Het
Zbp1	A	G	2: 173,051,006 (GRCm39)	F288S	probably damaging	Het
Zc3h11a	T	A	1: 133,568,436 (GRCm39)	Q71L	probably damaging	Het
Zfp40	G	A	17: 23,396,008 (GRCm39)	T193I	possibly damaging	Het
Zfp607a	T	C	7: 27,578,078 (GRCm39)	Y383H	probably benign	Het
Zfp622	T	A	15: 25,987,128 (GRCm39)	Y82*	probably null	Het
Zfp964	T	C	8: 70,116,665 (GRCm39)	F422L	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
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
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'- GCAACAAGGATTTGGCTTTGC -3'
(R):5'- ACTTCGAGACCCTCTTGCAAG -3'

Sequencing Primer
(F):5'- AAGTCACTTCGGCCTCACG -3'
(R):5'- TCTTGCAAGGGGAATATCCAC -3'

Posted On

2016-02-04