Mutagenetix > Incidental Mutation

Incidental Mutation 'R5493:Shox2'

432160

Institutional Source

Beutler Lab

Gene Symbol

Shox2

Ensembl Gene

ENSMUSG00000027833

Gene Name

SHOX homeobox 2

Synonyms

Og12x, Prx3, 6330543G17Rik

MMRRC Submission

043054-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5493 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

66879060-66889104 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to G at 66888796 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Arginine at position 32 (G32R)

Ref Sequence

ENSEMBL: ENSMUSP00000029422 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029422] [ENSMUST00000046542] [ENSMUST00000065047] [ENSMUST00000065074] [ENSMUST00000160504] [ENSMUST00000161726] [ENSMUST00000162036] [ENSMUST00000195261] [ENSMUST00000162439] [ENSMUST00000162362] [ENSMUST00000162060] [ENSMUST00000162693]

AlphaFold

P70390

Predicted Effect

probably damaging
Transcript: ENSMUST00000029422
AA Change: G32R

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000029422
Gene: ENSMUSG00000027833
AA Change: G32R

Domain	Start	End	E-Value	Type
low complexity region	57	90	N/A	INTRINSIC
HOX	140	202	1.8e-28	SMART
low complexity region	258	273	N/A	INTRINSIC
Pfam:OAR	310	327	3.3e-10	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000046542

SMART Domains

Protein: ENSMUSP00000047077
Gene: ENSMUSG00000034544

Domain	Start	End	E-Value	Type
low complexity region	3	116	N/A	INTRINSIC
coiled coil region	138	191	N/A	INTRINSIC
low complexity region	223	236	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000065047

SMART Domains

Protein: ENSMUSP00000066967
Gene: ENSMUSG00000034544

Domain	Start	End	E-Value	Type
low complexity region	3	109	N/A	INTRINSIC
coiled coil region	122	175	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000065074

SMART Domains

Protein: ENSMUSP00000066797
Gene: ENSMUSG00000034544

Domain	Start	End	E-Value	Type
low complexity region	3	95	N/A	INTRINSIC
low complexity region	98	159	N/A	INTRINSIC
coiled coil region	180	233	N/A	INTRINSIC
low complexity region	265	278	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000160504

SMART Domains

Protein: ENSMUSP00000124925
Gene: ENSMUSG00000034544

Domain	Start	End	E-Value	Type
low complexity region	3	59	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000161726

SMART Domains

Protein: ENSMUSP00000124347
Gene: ENSMUSG00000034544

Domain	Start	End	E-Value	Type
low complexity region	3	95	N/A	INTRINSIC
low complexity region	98	159	N/A	INTRINSIC
coiled coil region	180	233	N/A	INTRINSIC
low complexity region	265	278	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000162036

SMART Domains

Protein: ENSMUSP00000125468
Gene: ENSMUSG00000034544

Domain	Start	End	E-Value	Type
low complexity region	3	95	N/A	INTRINSIC
low complexity region	98	159	N/A	INTRINSIC
coiled coil region	180	233	N/A	INTRINSIC
low complexity region	265	278	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162620

Predicted Effect

probably benign
Transcript: ENSMUST00000195261

SMART Domains

Protein: ENSMUSP00000141625
Gene: ENSMUSG00000027833

Domain	Start	End	E-Value	Type
HOX	11	73	9e-31	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000162439

SMART Domains

Protein: ENSMUSP00000124924
Gene: ENSMUSG00000027833

Domain	Start	End	E-Value	Type
HOX	11	73	1.8e-28	SMART
low complexity region	117	132	N/A	INTRINSIC
Pfam:OAR	167	187	9.7e-11	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000162362

SMART Domains

Protein: ENSMUSP00000123699
Gene: ENSMUSG00000034544

Domain	Start	End	E-Value	Type
low complexity region	3	59	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000162060

SMART Domains

Protein: ENSMUSP00000125031
Gene: ENSMUSG00000027833

Domain	Start	End	E-Value	Type
HOX	11	73	1.8e-28	SMART
low complexity region	117	132	N/A	INTRINSIC
Pfam:OAR	167	187	9.7e-11	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000162098

SMART Domains

Protein: ENSMUSP00000123838
Gene: ENSMUSG00000027833

Domain	Start	End	E-Value	Type
low complexity region	1	11	N/A	INTRINSIC
HOX	61	123	1.8e-28	SMART
low complexity region	167	182	N/A	INTRINSIC
Pfam:OAR	219	236	1e-10	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000162693

SMART Domains

Protein: ENSMUSP00000125547
Gene: ENSMUSG00000034544

Domain	Start	End	E-Value	Type
low complexity region	3	88	N/A	INTRINSIC
low complexity region	96	157	N/A	INTRINSIC
coiled coil region	178	231	N/A	INTRINSIC

Meta Mutation Damage Score

0.3901

Coding Region Coverage

1x: 98.3%
3x: 97.3%
10x: 95.1%
20x: 90.4%

Validation Efficiency

99% (80/81)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the homeobox family of genes that encode proteins containing a 60-amino acid residue motif that represents a DNA binding domain. Homeobox genes have been characterized extensively as transcriptional regulators involved in pattern formation in both invertebrate and vertebrate species. Several human genetic disorders are caused by aberrations in human homeobox genes. This locus represents a pseudoautosomal homeobox gene that is thought to be responsible for idiopathic short stature, and it is implicated in the short stature phenotype of Turner syndrome patients. This gene is considered to be a candidate gene for Cornelia de Lange syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2009]
PHENOTYPE: Homozygous null mice display incomplete penetrance of embryonic lethality during organogenesis and incomplete clefting of the anterior part of the palate. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2510009E07Rik	A	G	16: 21,471,993 (GRCm39)	S236P	possibly damaging	Het
A830018L16Rik	C	T	1: 11,615,431 (GRCm39)	R135C	probably damaging	Het
Agpat3	A	G	10: 78,120,069 (GRCm39)	V155A	possibly damaging	Het
Aldh18a1	C	T	19: 40,539,734 (GRCm39)	R747Q	probably damaging	Het
Aloxe3	A	T	11: 69,019,443 (GRCm39)	R119*	probably null	Het
Asap1	A	G	15: 64,002,000 (GRCm39)	V460A	possibly damaging	Het
Bicral	C	A	17: 47,112,620 (GRCm39)	R860L	possibly damaging	Het
Cd180	T	A	13: 102,842,649 (GRCm39)	I565N	probably benign	Het
Cdk13	T	C	13: 17,978,147 (GRCm39)		probably benign	Het
Cdkn2d	T	C	9: 21,200,303 (GRCm39)	D156G	probably benign	Het
Clrn1	A	G	3: 58,753,837 (GRCm39)	S175P	probably damaging	Het
Coro7	A	G	16: 4,450,351 (GRCm39)	L535S	probably damaging	Het
Cse1l	A	G	2: 166,783,110 (GRCm39)		probably benign	Het
Cyp2a12	T	C	7: 26,728,550 (GRCm39)	L7P	unknown	Het
D130043K22Rik	A	G	13: 25,047,586 (GRCm39)	Y377C	probably damaging	Het
Dctn1	G	T	6: 83,159,546 (GRCm39)	R8L	possibly damaging	Het
Duox2	T	C	2: 122,111,977 (GRCm39)	Q1341R	probably damaging	Het
Eif2b3	A	G	4: 116,943,919 (GRCm39)	D447G	possibly damaging	Het
Eif4a3l1	C	G	6: 136,306,555 (GRCm39)	R339G	probably damaging	Het
Fbxw25	T	C	9: 109,481,984 (GRCm39)	Y234C	probably benign	Het
Gcnt2	A	G	13: 41,107,076 (GRCm39)	N315S	possibly damaging	Het
Gm20730	A	T	6: 43,058,746 (GRCm39)	V22E	possibly damaging	Het
Gm4847	T	A	1: 166,457,890 (GRCm39)	I488F	probably damaging	Het
Gmds	A	T	13: 32,124,488 (GRCm39)	M290K	probably benign	Het
Gtf3c1	T	C	7: 125,269,716 (GRCm39)	N699S	probably damaging	Het
Hk3	A	G	13: 55,158,984 (GRCm39)	V479A	probably damaging	Het
Ifnlr1	G	A	4: 135,432,877 (GRCm39)	V438M	probably benign	Het
Il12rb1	C	A	8: 71,262,483 (GRCm39)	P26T	probably benign	Het
Il4i1	G	T	7: 44,489,477 (GRCm39)	R414L	possibly damaging	Het
Ipo4	T	C	14: 55,868,327 (GRCm39)	N490S	probably benign	Het
Kcnmb2	A	G	3: 32,252,291 (GRCm39)	E164G	probably damaging	Het
Kcns1	G	A	2: 164,009,899 (GRCm39)	L287F	probably benign	Het
Kdm1a	ACC	AC	4: 136,284,732 (GRCm39)		probably null	Het
Klk14	G	A	7: 43,341,501 (GRCm39)	C51Y	probably damaging	Het
Knl1	T	A	2: 118,899,211 (GRCm39)	I304K	probably damaging	Het
Ksr2	G	T	5: 117,846,175 (GRCm39)	V681F	probably damaging	Het
Lypd2	T	C	15: 74,606,127 (GRCm39)	T4A	probably benign	Het
Man1a	A	G	10: 53,950,576 (GRCm39)	V182A	probably benign	Het
Or12j4	A	T	7: 140,046,720 (GRCm39)	D202V	probably damaging	Het
Or13e8	A	G	4: 43,696,225 (GRCm39)	F316S	possibly damaging	Het
Or2w2	A	T	13: 21,758,042 (GRCm39)	C195S	probably damaging	Het
Or51f5	A	T	7: 102,424,315 (GRCm39)	R195W	probably benign	Het
Or56b1b	T	C	7: 108,164,774 (GRCm39)	D76G	probably benign	Het
Pcdha2	C	A	18: 37,072,562 (GRCm39)	F64L	probably damaging	Het
Pgap3	G	C	11: 98,281,540 (GRCm39)	F168L	possibly damaging	Het
Pip5k1b	T	C	19: 24,416,439 (GRCm39)	N16S	probably benign	Het
Ppip5k1	T	A	2: 121,167,253 (GRCm39)	H41L	probably damaging	Het
Ppp1r9a	A	G	6: 5,159,702 (GRCm39)	R1080G	probably damaging	Het
Qrich2	A	C	11: 116,336,774 (GRCm39)		probably null	Het
Rbl2	C	T	8: 91,842,447 (GRCm39)	P1034L	probably damaging	Het
Rbpjl	GCC	GC	2: 164,256,330 (GRCm39)		probably null	Het
Rin2	A	G	2: 145,702,629 (GRCm39)	S442G	probably damaging	Het
Rtca	C	T	3: 116,293,280 (GRCm39)	R71Q	probably benign	Het
Serpind1	A	T	16: 17,157,902 (GRCm39)	N366I	probably damaging	Het
Sp3	T	A	2: 72,768,466 (GRCm39)	N766Y	probably damaging	Het
Spag7	T	A	11: 70,560,059 (GRCm39)	S17C	probably null	Het
Stk25	A	T	1: 93,563,031 (GRCm39)	F7I	probably benign	Het
Tbx15	G	A	3: 99,259,880 (GRCm39)	G584S	probably benign	Het
Tenm2	T	C	11: 36,755,503 (GRCm39)	D165G	probably benign	Het
Tox2	C	A	2: 163,046,649 (GRCm39)	S42*	probably null	Het
Vmn1r39	A	G	6: 66,781,754 (GRCm39)	V188A	probably damaging	Het
Zbtb5	A	T	4: 44,993,941 (GRCm39)	M481K	probably benign	Het
Zfp26	T	C	9: 20,355,615 (GRCm39)	T56A	possibly damaging	Het
Zfp459	C	A	13: 67,556,498 (GRCm39)	C195F	probably damaging	Het
Zfp703	C	T	8: 27,469,233 (GRCm39)	P299L	probably damaging	Het
Zfp764	A	G	7: 127,004,105 (GRCm39)	I342T	probably benign	Het
Zfp942	T	C	17: 22,151,985 (GRCm39)	N7D	probably null	Het

Other mutations in Shox2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00334:Shox2	APN	3	66,888,774 (GRCm39)	missense	possibly damaging	0.49
IGL00813:Shox2	APN	3	66,882,777 (GRCm39)	missense	probably damaging	1.00
IGL01534:Shox2	APN	3	66,885,696 (GRCm39)	missense	probably benign	0.01
IGL01583:Shox2	APN	3	66,881,104 (GRCm39)	unclassified	probably benign
R0306:Shox2	UTSW	3	66,881,167 (GRCm39)	missense	probably damaging	0.98
R0374:Shox2	UTSW	3	66,881,184 (GRCm39)	missense	probably damaging	0.98
R0625:Shox2	UTSW	3	66,888,877 (GRCm39)	critical splice donor site	probably null
R0774:Shox2	UTSW	3	66,881,144 (GRCm39)	missense	probably damaging	1.00
R1102:Shox2	UTSW	3	66,885,628 (GRCm39)	missense	probably damaging	1.00
R1192:Shox2	UTSW	3	66,881,243 (GRCm39)	nonsense	probably null
R2354:Shox2	UTSW	3	66,888,822 (GRCm39)	missense	possibly damaging	0.94
R2518:Shox2	UTSW	3	66,885,692 (GRCm39)	missense	possibly damaging	0.83
R4163:Shox2	UTSW	3	66,881,104 (GRCm39)	unclassified	probably benign
R4976:Shox2	UTSW	3	66,881,008 (GRCm39)	unclassified	probably benign
R5423:Shox2	UTSW	3	66,881,087 (GRCm39)	unclassified	probably benign
R6528:Shox2	UTSW	3	66,888,618 (GRCm39)	missense	probably benign	0.00
RF020:Shox2	UTSW	3	66,881,146 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ATCCCGGTATCTCCCAAAGC -3'
(R):5'- GAAGCATCAGTTCCCATTTCCC -3'

Sequencing Primer
(F):5'- ATGTCCAGCTCCCGGAC -3'
(R):5'- CTGCCCCATTGATGTGTTATTATTG -3'

Posted On

2016-10-05