Mutagenetix > Incidental Mutation

Incidental Mutation 'R5542:Crx'

436029

Institutional Source

Beutler Lab

Gene Symbol

Crx

Ensembl Gene

ENSMUSG00000041578

Gene Name

cone-rod homeobox

Synonyms

Crx1

MMRRC Submission

043100-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.375) question?

Stock #

R5542 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

15599872-15613880 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 15602262 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Cysteine at position 139 (R139C)

Ref Sequence

ENSEMBL: ENSMUSP00000134400 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000044434] [ENSMUST00000132563] [ENSMUST00000172758] [ENSMUST00000174318]

AlphaFold

O54751

Predicted Effect

probably damaging
Transcript: ENSMUST00000044434
AA Change: R115C

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000043436
Gene: ENSMUSG00000041578
AA Change: R115C

Domain	Start	End	E-Value	Type
HOX	39	101	2.39e-24	SMART
low complexity region	139	153	N/A	INTRINSIC
Pfam:TF_Otx	164	250	1.1e-15	PFAM
internal_repeat_1	260	278	1.41e-5	PROSPERO
internal_repeat_1	279	296	1.41e-5	PROSPERO

Predicted Effect

probably damaging
Transcript: ENSMUST00000132563
AA Change: R115C

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000133833
Gene: ENSMUSG00000041578
AA Change: R115C

Domain	Start	End	E-Value	Type
HOX	39	101	2.39e-24	SMART
low complexity region	139	153	N/A	INTRINSIC
low complexity region	196	207	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000172758

SMART Domains

Protein: ENSMUSP00000134463
Gene: ENSMUSG00000041578

Domain	Start	End	E-Value	Type
HOX	39	74	6.07e-1	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000174318
AA Change: R139C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000134400
Gene: ENSMUSG00000041578
AA Change: R139C

Domain	Start	End	E-Value	Type
HOX	39	101	2.39e-24	SMART
low complexity region	139	153	N/A	INTRINSIC
Pfam:TF_Otx	164	250	1.1e-15	PFAM
internal_repeat_1	260	278	1.41e-5	PROSPERO
internal_repeat_1	279	296	1.41e-5	PROSPERO

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174358

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.3%
20x: 95.1%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a photoreceptor-specific transcription factor which plays a role in the differentiation of photoreceptor cells. This homeodomain protein is necessary for the maintenance of normal cone and rod function. Mutations in this gene are associated with photoreceptor degeneration, Leber congenital amaurosis type III and the autosomal dominant cone-rod dystrophy 2. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some variants has not been determined. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit a lack of photoreceptor outer segments and rod and cone activity, reduced expression of several photoreceptor- and pineal-specific genes, and altered circadian behavior. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadacl2	C	T	3: 59,932,484 (GRCm39)	T333I	probably damaging	Het
Acacb	C	T	5: 114,333,798 (GRCm39)	R574C	probably damaging	Het
Actr10	T	C	12: 71,001,430 (GRCm39)		probably benign	Het
Ankdd1a	T	A	9: 65,411,472 (GRCm39)		probably null	Het
Anks4b	C	T	7: 119,781,646 (GRCm39)	Q226*	probably null	Het
AW146154	C	A	7: 41,130,801 (GRCm39)	G105V	probably benign	Het
Cdh4	T	A	2: 179,502,019 (GRCm39)	N326K	probably damaging	Het
Cnbd1	T	C	4: 18,860,517 (GRCm39)	T410A	possibly damaging	Het
Cndp2	A	T	18: 84,690,201 (GRCm39)	M247K	probably damaging	Het
Ctrc	A	G	4: 141,571,037 (GRCm39)	Y68H	probably damaging	Het
Ddx4	T	C	13: 112,757,779 (GRCm39)	D326G	probably damaging	Het
Edem1	C	T	6: 108,831,290 (GRCm39)	R584C	possibly damaging	Het
Emcn	A	G	3: 137,085,638 (GRCm39)	T79A	probably benign	Het
Ext1	C	A	15: 52,939,213 (GRCm39)	W612L	probably damaging	Het
Fbrsl1	C	T	5: 110,526,307 (GRCm39)	G437R	probably damaging	Het
Fbxo7	A	C	10: 85,869,149 (GRCm39)	Q201P	probably benign	Het
Fbxo9	T	C	9: 78,008,938 (GRCm39)	M12V	possibly damaging	Het
Fcgbpl1	A	T	7: 27,854,914 (GRCm39)	I1847F	probably damaging	Het
Flii	A	G	11: 60,609,688 (GRCm39)	S640P	probably benign	Het
Fsip2	A	T	2: 82,812,207 (GRCm39)	N2842I	possibly damaging	Het
Fst	G	T	13: 114,592,241 (GRCm39)	Q159K	probably damaging	Het
Fuom	A	T	7: 139,680,025 (GRCm39)	*109R	probably null	Het
Hhipl2	A	G	1: 183,214,055 (GRCm39)	D377G	probably damaging	Het
Hspa14	A	G	2: 3,503,560 (GRCm39)	V116A	possibly damaging	Het
Ighm	A	G	12: 113,382,601 (GRCm39)		probably benign	Het
Ighv1-85	T	A	12: 115,963,847 (GRCm39)	Y51F	probably benign	Het
Ighv2-3	A	T	12: 113,574,833 (GRCm39)	D107E	probably benign	Het
Ighv2-6-8	T	A	12: 113,760,187 (GRCm39)	M1L	probably benign	Het
Ipo5	T	C	14: 121,163,683 (GRCm39)	V247A	probably benign	Het
Itga9	T	C	9: 118,672,729 (GRCm39)	F154L	possibly damaging	Het
Itprid1	C	A	6: 55,955,380 (GRCm39)	P996Q	probably damaging	Het
Knl1	T	A	2: 118,898,829 (GRCm39)	C177S	possibly damaging	Het
Lrrc17	G	A	5: 21,780,156 (GRCm39)	G377S	probably damaging	Het
Marveld3	A	T	8: 110,675,249 (GRCm39)	I189K	probably benign	Het
Msantd2	G	A	9: 37,428,555 (GRCm39)	G185R	probably damaging	Het
Mtcl1	G	A	17: 66,691,354 (GRCm39)		probably benign	Het
Muc21	T	C	17: 35,933,395 (GRCm39)		probably benign	Het
Mycbpap	A	T	11: 94,398,572 (GRCm39)		probably null	Het
Nbeal1	A	G	1: 60,316,353 (GRCm39)	D1852G	probably benign	Het
Ndc80	A	T	17: 71,807,276 (GRCm39)	V560D	probably benign	Het
Nscme3l	A	T	19: 5,553,463 (GRCm39)	V106D	probably damaging	Het
Or1e25	T	A	11: 73,494,030 (GRCm39)	V208E	possibly damaging	Het
Or2t48	A	C	11: 58,420,710 (GRCm39)	V34G	probably benign	Het
Or56a3	A	T	7: 104,735,565 (GRCm39)	D214V	probably damaging	Het
Or6a2	A	T	7: 106,600,286 (GRCm39)	S260R	probably damaging	Het
Or9i1b	T	C	19: 13,896,411 (GRCm39)	V9A	probably benign	Het
Pcdhga4	A	T	18: 37,819,651 (GRCm39)	Y400F	probably damaging	Het
Pkd2	A	G	5: 104,634,515 (GRCm39)		silent	Het
Plxna4	T	A	6: 32,183,165 (GRCm39)	I913F	probably damaging	Het
Psmc1	T	C	12: 100,086,399 (GRCm39)		probably null	Het
Robo2	G	A	16: 73,695,853 (GRCm39)	T1430I	probably benign	Het
Safb2	G	A	17: 56,882,647 (GRCm39)	R329C	probably damaging	Het
Septin14	T	C	5: 129,774,926 (GRCm39)	H83R	probably damaging	Het
Slc16a10	A	G	10: 39,952,784 (GRCm39)	F237L	probably benign	Het
Slc37a1	A	T	17: 31,559,236 (GRCm39)	T439S	probably damaging	Het
Slc6a6	T	C	6: 91,712,170 (GRCm39)	F233S	probably damaging	Het
Smyd3	A	T	1: 179,238,024 (GRCm39)	D114E	probably benign	Het
Sned1	T	C	1: 93,199,324 (GRCm39)	I468T	probably benign	Het
Speer4a1	T	A	5: 26,241,736 (GRCm39)	N130I	probably damaging	Het
Tdrd7	T	C	4: 46,029,757 (GRCm39)	V1030A	probably benign	Het
Trip12	A	T	1: 84,727,065 (GRCm39)	D1135E	probably damaging	Het
Tsga10	T	A	1: 37,800,598 (GRCm39)	D542V	probably damaging	Het
Ubqlnl	G	A	7: 103,798,904 (GRCm39)	Q198*	probably null	Het
Unc93a2	A	T	17: 7,637,187 (GRCm39)	C334S	probably benign	Het
Usp46	A	T	5: 74,189,902 (GRCm39)	M43K	probably benign	Het
Vmn1r175	A	T	7: 23,508,531 (GRCm39)	I32N	possibly damaging	Het
Vmn1r29	C	T	6: 58,285,108 (GRCm39)	T276I	probably benign	Het
Vmn1r81	A	T	7: 11,994,034 (GRCm39)	D191E	probably damaging	Het
Zbtb5	C	A	4: 44,995,052 (GRCm39)	V111F	probably damaging	Het
Zfp12	C	T	5: 143,230,240 (GRCm39)	P189L	possibly damaging	Het
Zfp729b	A	G	13: 67,739,140 (GRCm39)	F1042L	probably benign	Het

Other mutations in Crx

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
Typhlotic	UTSW	7	15,602,032 (GRCm39)	nonsense	probably null
R0437:Crx	UTSW	7	15,605,071 (GRCm39)	nonsense	probably null
R0729:Crx	UTSW	7	15,605,058 (GRCm39)	splice site	probably benign
R1601:Crx	UTSW	7	15,601,736 (GRCm39)	splice site	probably null
R1898:Crx	UTSW	7	15,602,148 (GRCm39)	missense	probably damaging	1.00
R1933:Crx	UTSW	7	15,602,301 (GRCm39)	nonsense	probably null
R1988:Crx	UTSW	7	15,603,272 (GRCm39)	missense	possibly damaging	0.95
R5272:Crx	UTSW	7	15,602,210 (GRCm39)	missense	probably damaging	0.99
R5326:Crx	UTSW	7	15,602,262 (GRCm39)	missense	probably damaging	1.00
R6134:Crx	UTSW	7	15,602,032 (GRCm39)	nonsense	probably null
R7313:Crx	UTSW	7	15,601,857 (GRCm39)	missense	probably damaging	1.00
R8458:Crx	UTSW	7	15,602,031 (GRCm39)	missense	possibly damaging	0.56
R9619:Crx	UTSW	7	15,602,185 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- TCATGGCATAAGGGGCTGAG -3'
(R):5'- GTGTGGGTCTTACCATCAGC -3'

Sequencing Primer
(F):5'- ACTAGGCCGGCTCTCTG -3'
(R):5'- GGGTCTTACCATCAGCTTTGTCTG -3'

Posted On

2016-10-24