Mutagenetix > Incidental Mutation

Incidental Mutation 'RF040:Cdx1'

604793

Institutional Source

Beutler Lab

Gene Symbol

Cdx1

Ensembl Gene

ENSMUSG00000024619

Gene Name

caudal type homeobox 1

Synonyms

Cdx-1, Cdx

Accession Numbers

Essential gene?

Probably essential (E-score: 0.932) question?

Stock #

RF040 (G1)

Quality Score

217.468

Status

Not validated

Chromosome

Chromosomal Location

61151934-61169271 bp(-) (GRCm39)

Type of Mutation

small insertion (2 aa in frame mutation)

DNA Base Change (assembly)

CTGCTG to CTGCTGATGCTG at 61152942 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000025521 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025521]

AlphaFold

P18111

Predicted Effect

probably benign
Transcript: ENSMUST00000025521

SMART Domains

Protein: ENSMUSP00000025521
Gene: ENSMUSG00000024619

Domain	Start	End	E-Value	Type
Pfam:Caudal_act	13	146	4.8e-31	PFAM
HOX	154	216	1.3e-25	SMART
low complexity region	217	246	N/A	INTRINSIC

Coding Region Coverage

1x: 99.8%
3x: 99.7%
10x: 99.4%
20x: 98.9%

Validation Efficiency

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 caudal-related homeobox transcription factor gene family. The encoded DNA-binding protein regulates intestine-specific gene expression and enterocyte differentiation. It has been shown to induce expression of the intestinal alkaline phosphatase gene, and inhibit beta-catenin/T-cell factor transcriptional activity. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutation of this gene results in abnormalities of the basiocciptal bone, vertebrae, and ribs. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A030005L19Rik	TGCTGTG	TGCTGTGACAGCTGTG	1: 82,891,298 (GRCm39)		probably benign	Het
A030005L19Rik	G	GTGGCTGCTC	1: 82,891,311 (GRCm39)		probably benign	Het
Brme1	TG	TGTCAGGGCAGCAGCAG	8: 84,894,204 (GRCm39)		probably benign	Het
Cacna1f	CTGAATTGGTTCCCAGACCCGTGT	CT	X: 7,485,210 (GRCm39)		probably null	Het
Calhm1	C	CTGTGGCTGTGGA	19: 47,129,716 (GRCm39)		probably benign	Het
Cyb5r4	ACACACTGCCCAGGGATGTGACAGACACACTGCCCAGGGA	ACACACTGCCCAGGGATGTGACAGCCACACTGCCCAGGGATGTGACAGACACACTGCCCAGGGA	9: 86,922,462 (GRCm39)		probably benign	Het
Dbr1	GAGGAG	GAGGAGTAGGAG	9: 99,465,750 (GRCm39)		probably null	Het
Dnajc2	TAGTTG	T	5: 21,962,695 (GRCm39)		probably null	Het
Fgd6	ATT	A	10: 93,880,187 (GRCm39)		probably null	Het
Flywch1	CTCCTGGTGT	CTCCTGGTGTGGGGAGGCTACGTACTCACCCAGTCCTGGTGT	17: 23,981,143 (GRCm39)		probably null	Het
Gab3	CTT	CTTTTT	X: 74,043,633 (GRCm39)		probably benign	Het
Garin5a	C	CGGGGTCAGAGGGAGGAAGGCTGGATCCTGGATACA	7: 44,149,945 (GRCm39)		probably null	Het
Garin5a	GGGAGGA	GGGAGGAAGGCTGGATCCTGGATACCTGGGTCTGATGGAGGA	7: 44,149,955 (GRCm39)		probably null	Het
Gm40460	CACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAG	CACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAG	7: 141,794,554 (GRCm39)		probably benign	Het
Gykl1	G	A	18: 52,827,488 (GRCm39)	R232Q	probably benign	Het
Heatr3	TAT	TATTGAT	8: 88,883,085 (GRCm39)		probably benign	Het
Kmt2e	TTT	TTTTCTT	5: 23,683,507 (GRCm39)		probably benign	Het
Luzp1	A	AGGTGGCCTCTTCAGC	4: 136,270,507 (GRCm39)		probably benign	Het
Mamld1	AACA	AACAACA	X: 70,162,420 (GRCm39)		probably benign	Het
Mast4	CCTCGGGGACAAGCTGTGAGTTGGGGAAC	CC	13: 102,875,749 (GRCm39)		probably benign	Het
Med12l	AGC	AGCCGC	3: 59,183,388 (GRCm39)		probably benign	Het
Med12l	GCA	GCATCA	3: 59,183,410 (GRCm39)		probably benign	Het
Mn1	CAG	CAGAAG	5: 111,567,571 (GRCm39)		probably benign	Het
Morn4	GCAGTGAG	GCAGTGAGTCAGTCAGTGAG	19: 42,064,550 (GRCm39)		probably null	Het
Ncoa6	TGCAGC	TGC	2: 155,263,651 (GRCm39)		probably benign	Het
Nlrp3	GGGTA	G	11: 59,449,378 (GRCm39)		probably null	Het
Nolc1	AGCAGCAGC	AGCAGCAGCCGCAGCAGC	19: 46,069,802 (GRCm39)		probably benign	Het
Nusap1	TTAGCAGTGAGGAGCAAGCTGAGA	TTAGCAGTGAGGAGCAAGCTGAGATACACGGTAGCAGTGAGGAGCAAGCTGAGA	2: 119,458,068 (GRCm39)		probably benign	Het
Or10j2	GTGACATC	G	1: 173,098,276 (GRCm39)		probably null	Het
Or52z15	ACTTGCTGATATCTT	ACTT	7: 103,332,145 (GRCm39)		probably null	Het
Osmr	TTCT	TTCTTCT	15: 6,867,182 (GRCm39)		probably benign	Het
Padi3	TCTCAC	TC	4: 140,520,283 (GRCm39)		probably benign	Het
Pdik1l	AC	ACCACCGC	4: 134,006,826 (GRCm39)		probably benign	Het
Rpgrip1	AGGAAGAGG	AG	14: 52,386,994 (GRCm39)		probably null	Het
Rragd	CATGCCTTTCATTCTA	C	4: 32,995,150 (GRCm39)		probably benign	Het
Ryr3	CTGA	C	2: 112,740,869 (GRCm39)		probably benign	Het
Sh3pxd2b	CCTGTG	CCTGTGTCTGTG	11: 32,373,055 (GRCm39)		probably benign	Het
Slc39a4	TGTGGTC	TGTGGTCATCATGATCACCATGGTCACCATGATCACGGTGGTC	15: 76,499,066 (GRCm39)		probably benign	Het
Smarca2	GC	GCCCCACC	19: 26,608,422 (GRCm39)		probably benign	Het
Spata31f3	TCATTCAACACTTTGGAGAGCTCTGAACTCTGGCCATTCAACACTTTGGAGAGCTCTGAACTCTGGCCATTCAACACTTTGGAGAGCTCTGAACTCTGGTCATTCAACACTTTGG	TCATTCAACACTTTGGAGAGCTCTGAACTCTGGCCATTCAACACTTTGGAGAGCTCTGAACTCTGGTCATTCAACACTTTGG	4: 42,871,823 (GRCm39)		probably benign	Het
Sprr2b	CAGTATGCTGTGAGCCTTGTCCTCCT	C	3: 92,224,871 (GRCm39)		probably null	Het
Sry	GCTG	GCTGGTGGTGGTGGTCATGGAACTG	Y: 2,662,590 (GRCm39)		probably benign	Het
Tcof1	CT	CTATT	18: 60,961,480 (GRCm39)		probably benign	Het
Tcof1	GC	GCTGCTGAGATGGGCACTTTCCCAGAGATCCCCTTGTC	18: 60,966,655 (GRCm39)		probably benign	Het
Tfeb	AGC	AGCCGC	17: 48,097,036 (GRCm39)		probably benign	Het
Tfeb	GCA	GCATCA	17: 48,097,037 (GRCm39)		probably benign	Het
Tfeb	GCA	GCAACA	17: 48,097,022 (GRCm39)		probably benign	Het
Tfeb	CAG	CAGGAG	17: 48,097,035 (GRCm39)		probably benign	Het
Tgoln1	T	TCACCTCCCGTGGTCTTGCCAGAAG	6: 72,593,057 (GRCm39)		probably benign	Het
Tmem59	TTTGTTT	TTTGTTTGGTTGTTT	4: 107,047,723 (GRCm39)		probably benign	Het
Trappc9	TGCTGCTGCTGCTGCTGCTGCTGCTGCTGC	TGCTGCTGCTGCTGCGGCTGCTGCTGCTGCTGCTGCTGCTGCTGC	15: 72,673,141 (GRCm39)		probably benign	Het
Triobp	CAA	CAACCCCAGGACTCCCTGTGCCCAACGGGGGAA	15: 78,851,263 (GRCm39)		probably benign	Het
Xirp2	TT	TTTAT	2: 67,355,888 (GRCm39)		probably benign	Het
Zfhx3	CAGCA	CAGCAACAGGAGCA	8: 109,682,733 (GRCm39)		probably benign	Het

Other mutations in Cdx1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
E0370:Cdx1	UTSW	18	61,153,501 (GRCm39)	missense	probably damaging	1.00
FR4449:Cdx1	UTSW	18	61,152,953 (GRCm39)	small insertion	probably benign
FR4737:Cdx1	UTSW	18	61,152,950 (GRCm39)	small insertion	probably benign
FR4737:Cdx1	UTSW	18	61,152,946 (GRCm39)	small insertion	probably benign
FR4976:Cdx1	UTSW	18	61,152,941 (GRCm39)	small insertion	probably benign
FR4976:Cdx1	UTSW	18	61,152,939 (GRCm39)	small insertion	probably benign
R0218:Cdx1	UTSW	18	61,153,436 (GRCm39)	splice site	probably benign
R0481:Cdx1	UTSW	18	61,153,564 (GRCm39)	missense	probably damaging	1.00
R1776:Cdx1	UTSW	18	61,169,086 (GRCm39)	missense	probably benign	0.01
R1914:Cdx1	UTSW	18	61,152,970 (GRCm39)	missense	probably benign	0.01
R1915:Cdx1	UTSW	18	61,152,970 (GRCm39)	missense	probably benign	0.01
R2094:Cdx1	UTSW	18	61,168,984 (GRCm39)	missense	possibly damaging	0.85
R4191:Cdx1	UTSW	18	61,153,510 (GRCm39)	missense	possibly damaging	0.88
R5671:Cdx1	UTSW	18	61,152,971 (GRCm39)	missense	probably benign	0.01
R8145:Cdx1	UTSW	18	61,152,995 (GRCm39)	missense	probably damaging	1.00
RF036:Cdx1	UTSW	18	61,152,942 (GRCm39)	small insertion	probably benign
RF038:Cdx1	UTSW	18	61,152,942 (GRCm39)	small insertion	probably benign
RF039:Cdx1	UTSW	18	61,152,942 (GRCm39)	small insertion	probably benign
RF049:Cdx1	UTSW	18	61,152,938 (GRCm39)	small insertion	probably benign

Predicted Primers

PCR Primer
(F):5'- ACTCAGAACAGGTCCTTGGG -3'
(R):5'- GTCACAGAACACAGGAGCTC -3'

Sequencing Primer
(F):5'- TCCTTGGGCCCCAGAAAAG -3'
(R):5'- CTCTGGAGAACTGGGGCCTTG -3'

Posted On

2019-12-04