Mutagenetix > Incidental Mutation

Incidental Mutation 'R5364:Chrd'

423052

Institutional Source

Beutler Lab

Gene Symbol

Chrd

Ensembl Gene

ENSMUSG00000006958

Gene Name

chordin

Synonyms

Chd

MMRRC Submission

042942-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5364 (G1)

Quality Score

121

Status

Validated

Chromosome

Chromosomal Location

20551877-20561134 bp(+) (GRCm39)

Type of Mutation

start codon destroyed

DNA Base Change (assembly)

A to G at 20551898 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Valine at position 1 (M1V)

Ref Sequence

ENSEMBL: ENSMUSP00000156323 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000007171] [ENSMUST00000076422] [ENSMUST00000115423] [ENSMUST00000115437] [ENSMUST00000153299] [ENSMUST00000231636] [ENSMUST00000232217] [ENSMUST00000232646] [ENSMUST00000231826] [ENSMUST00000231698]

AlphaFold

Q9Z0E2

Predicted Effect

probably null
Transcript: ENSMUST00000007171
AA Change: M1V

SMART Domains

Protein: ENSMUSP00000007171
Gene: ENSMUSG00000006958
AA Change: M1V

Domain	Start	End	E-Value	Type
signal peptide	1	26	N/A	INTRINSIC
VWC	51	125	9.33e-2	SMART
CHRD	170	274	1.27e-14	SMART
CHRD	281	395	4.63e-17	SMART
CHRD	400	517	7.81e-24	SMART
CHRD	528	643	2.03e-31	SMART
low complexity region	676	687	N/A	INTRINSIC
VWC	701	758	4.69e-10	SMART
VWC	779	845	5.3e-9	SMART
VWC	867	927	1.68e-1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000076422

SMART Domains

Protein: ENSMUSP00000075756
Gene: ENSMUSG00000022847

Domain	Start	End	E-Value	Type
signal peptide	1	21	N/A	INTRINSIC
Pfam:EPO_TPO	24	188	9.4e-78	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000115423
AA Change: M1V

SMART Domains

Protein: ENSMUSP00000111083
Gene: ENSMUSG00000006958
AA Change: M1V

Domain	Start	End	E-Value	Type
signal peptide	1	26	N/A	INTRINSIC
VWC	51	125	9.33e-2	SMART
CHRD	170	274	1.27e-14	SMART
CHRD	281	395	4.63e-17	SMART
CHRD	400	517	7.81e-24	SMART
CHRD	528	605	3.92e-1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000115437

SMART Domains

Protein: ENSMUSP00000111097
Gene: ENSMUSG00000022847

Domain	Start	End	E-Value	Type
signal peptide	1	21	N/A	INTRINSIC
Pfam:EPO_TPO	25	193	5.4e-49	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000151150

Predicted Effect

probably null
Transcript: ENSMUST00000153299
AA Change: M1V

SMART Domains

Protein: ENSMUSP00000138259
Gene: ENSMUSG00000006958
AA Change: M1V

Domain	Start	End	E-Value	Type
signal peptide	1	26	N/A	INTRINSIC
VWC	51	125	9.33e-2	SMART
Blast:CHRD	170	236	1e-21	BLAST

Predicted Effect

probably null
Transcript: ENSMUST00000231636
AA Change: M1V

Predicted Effect

probably benign
Transcript: ENSMUST00000232217

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232104

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000231689

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232020

Predicted Effect

probably null
Transcript: ENSMUST00000232646
AA Change: M1V

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

Predicted Effect

probably benign
Transcript: ENSMUST00000231826

Predicted Effect

probably null
Transcript: ENSMUST00000231698
AA Change: M1V

PolyPhen 2 Score 0.026 (Sensitivity: 0.95; Specificity: 0.81)

Meta Mutation Damage Score

0.9528

Coding Region Coverage

1x: 99.3%
3x: 98.8%
10x: 97.6%
20x: 96.3%

Validation Efficiency

100% (102/102)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a secreted protein that dorsalizes early vertebrate embryonic tissues by binding to ventralizing TGF-beta-like bone morphogenetic proteins and sequestering them in latent complexes. The encoded protein may also have roles in organogenesis and during adulthood. It has been suggested that this gene could be a candidate gene for Cornelia de Lange syndrome. Reduced expression of this gene results in enhanced bone regeneration. Alternative splicing results in multiple transcript variants. Other alternative splice variants have been described but their full length sequence has not been determined. [provided by RefSeq, Jan 2015]
PHENOTYPE: Homozygotes for a targeted null mutation show some death prior to embryonic day 8.5, but most die perinatally with abnormalities of the skull, malformations of cervical and thoracic vertebrae, cardiovascular defects, and absence of parathyroid and thymus. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 91 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310022A10Rik	C	G	7: 27,278,192 (GRCm39)	T242R	probably damaging	Het
Abcc10	G	A	17: 46,616,577 (GRCm39)	R1205C	probably benign	Het
Acer1	A	G	17: 57,289,000 (GRCm39)	F37L	probably damaging	Het
Acp7	C	A	7: 28,310,448 (GRCm39)	G463V	probably benign	Het
Actr2	A	T	11: 20,050,797 (GRCm39)		probably benign	Het
Adam15	A	T	3: 89,252,902 (GRCm39)	I272K	probably damaging	Het
Adam1b	T	A	5: 121,638,946 (GRCm39)	I700F	possibly damaging	Het
Adam33	A	G	2: 130,896,392 (GRCm39)		probably null	Het
Ano1	T	C	7: 144,190,941 (GRCm39)	Y380C	probably damaging	Het
Arfgap3	A	C	15: 83,198,562 (GRCm39)	M307R	probably damaging	Het
Arhgap21	T	A	2: 20,854,533 (GRCm39)	R1610W	probably damaging	Het
Bbs2	A	G	8: 94,801,023 (GRCm39)	Y603H	probably benign	Het
Bbs9	G	T	9: 22,486,492 (GRCm39)		probably null	Het
Bcar3	A	C	3: 122,323,281 (GRCm39)	M779L	probably benign	Het
Bub3	A	T	7: 131,162,467 (GRCm39)	N10I	possibly damaging	Het
Cacna1c	T	G	6: 118,633,504 (GRCm39)	E1098D	probably benign	Het
Cacna1g	T	A	11: 94,307,684 (GRCm39)	M1738L	probably benign	Het
Camk2d	G	T	3: 126,574,069 (GRCm39)	G159C	probably damaging	Het
Ccdc51	A	T	9: 108,921,188 (GRCm39)	E358D	possibly damaging	Het
Cdc42bpa	A	G	1: 179,894,747 (GRCm39)	D309G	probably benign	Het
Cdhr3	A	T	12: 33,101,007 (GRCm39)	F468I	possibly damaging	Het
Cmtm1	CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT	CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT	8: 105,036,102 (GRCm39)		probably benign	Het
Dcdc2b	T	C	4: 129,502,963 (GRCm39)	Y253C	probably damaging	Het
Dclk1	A	C	3: 55,163,366 (GRCm39)	N153H	possibly damaging	Het
Dgkg	G	T	16: 22,419,211 (GRCm39)	S96R	probably benign	Het
Dnah9	A	G	11: 65,772,522 (GRCm39)	Y3737H	possibly damaging	Het
Elovl4	A	T	9: 83,672,076 (GRCm39)	I81N	probably benign	Het
Epha7	T	A	4: 28,950,557 (GRCm39)	Y791N	probably damaging	Het
Fam193a	C	A	5: 34,623,597 (GRCm39)	T1395N	probably benign	Het
Fbln5	A	T	12: 101,737,623 (GRCm39)	V141E	probably damaging	Het
Flii	T	C	11: 60,610,954 (GRCm39)	T492A	probably benign	Het
Fnip2	A	G	3: 79,388,475 (GRCm39)	I752T	probably benign	Het
Fpr3	T	C	17: 18,190,806 (GRCm39)	W26R	probably benign	Het
Gabrb1	A	T	5: 72,294,105 (GRCm39)	T460S	probably benign	Het
Gde1	T	C	7: 118,297,874 (GRCm39)	N4S	probably benign	Het
Ghitm	G	T	14: 36,847,156 (GRCm39)	T306K	probably benign	Het
Ghitm	A	T	14: 36,847,174 (GRCm39)	I300N	probably damaging	Het
Gm4787	G	C	12: 81,424,604 (GRCm39)	T518S	probably benign	Het
Iqcd	T	C	5: 120,738,332 (GRCm39)	I50T	probably damaging	Het
Itpripl1	G	A	2: 126,983,739 (GRCm39)	P128S	possibly damaging	Het
Jag2	C	A	12: 112,874,154 (GRCm39)	L1000F	probably damaging	Het
Klhdc4	A	T	8: 122,533,375 (GRCm39)		probably benign	Het
Klra5	A	G	6: 129,876,316 (GRCm39)	F164L	probably benign	Het
Larp1b	A	G	3: 40,931,658 (GRCm39)	Y288C	probably damaging	Het
Lrfn3	T	A	7: 30,055,078 (GRCm39)	E622D	possibly damaging	Het
Lyst	A	G	13: 13,831,439 (GRCm39)	D1621G	probably benign	Het
Mastl	T	C	2: 23,023,665 (GRCm39)	T353A	probably benign	Het
Mkln1	T	C	6: 31,473,647 (GRCm39)	Y130H	probably damaging	Het
Mms22l	T	A	4: 24,496,882 (GRCm39)		probably benign	Het
Mroh7	T	A	4: 106,548,840 (GRCm39)	M1008L	probably benign	Het
Nipal1	T	C	5: 72,825,243 (GRCm39)	V312A	probably damaging	Het
Nlrp5	T	A	7: 23,117,753 (GRCm39)	Y492*	probably null	Het
Odad1	T	A	7: 45,585,756 (GRCm39)	I105N	probably damaging	Het
Or1n1	T	C	2: 36,750,006 (GRCm39)	Y118C	probably damaging	Het
Otulinl	G	A	15: 27,660,031 (GRCm39)	Q24*	probably null	Het
Pcdhb11	T	A	18: 37,555,232 (GRCm39)	D187E	probably benign	Het
Pcdhb13	A	G	18: 37,576,561 (GRCm39)	Y313C	probably damaging	Het
Pdpn	G	A	4: 143,000,526 (GRCm39)	T102I	possibly damaging	Het
Pear1	A	T	3: 87,665,668 (GRCm39)	C120S	probably damaging	Het
Peg10	T	C	6: 4,756,128 (GRCm39)		probably benign	Het
Ppm1e	A	G	11: 87,128,007 (GRCm39)	W384R	probably benign	Het
Ppp1r10	C	T	17: 36,241,324 (GRCm39)	P700S	unknown	Het
Prl2c5	G	A	13: 13,357,627 (GRCm39)	R13K	probably benign	Het
Prmt3	C	A	7: 49,498,554 (GRCm39)	P487T	probably damaging	Het
Proser3	C	A	7: 30,245,573 (GRCm39)	A144S	possibly damaging	Het
Ptcd1	G	A	5: 145,088,241 (GRCm39)	T590I	probably damaging	Het
Rbsn	A	G	6: 92,170,958 (GRCm39)	V321A	probably damaging	Het
Slc40a1	C	A	1: 45,964,383 (GRCm39)	C14F	probably damaging	Het
Slc6a15	T	C	10: 103,229,369 (GRCm39)	I136T	probably damaging	Het
Slc7a4	A	G	16: 17,391,227 (GRCm39)	I449T	probably benign	Het
Snrnp48	T	A	13: 38,394,165 (GRCm39)		probably null	Het
Tada2a	A	G	11: 84,011,973 (GRCm39)	Y23H	probably benign	Het
Tbx15	A	T	3: 99,259,508 (GRCm39)	S460C	possibly damaging	Het
Tbx21	C	T	11: 96,992,304 (GRCm39)		probably null	Het
Tmcc2	T	G	1: 132,285,534 (GRCm39)	T376P	probably damaging	Het
Tmco4	G	A	4: 138,779,815 (GRCm39)	C420Y	probably damaging	Het
Tmem235	C	A	11: 117,755,020 (GRCm39)	Y157*	probably null	Het
Tmem63b	T	C	17: 45,975,653 (GRCm39)		probably benign	Het
Tnfrsf1a	T	C	6: 125,334,356 (GRCm39)	S92P	possibly damaging	Het
Top3b	A	T	16: 16,704,834 (GRCm39)	T397S	probably benign	Het
Trabd	C	A	15: 88,967,007 (GRCm39)		probably benign	Het
Trbv21	A	T	6: 41,179,764 (GRCm39)	I27L	possibly damaging	Het
Trim3	C	T	7: 105,268,276 (GRCm39)	V169M	probably damaging	Het
Ttn	T	C	2: 76,807,458 (GRCm39)	T92A	probably damaging	Het
Ttn	C	T	2: 76,738,860 (GRCm39)	S3893N	probably benign	Het
Uchl4	A	T	9: 64,142,821 (GRCm39)	I101F	possibly damaging	Het
Vmn1r5	T	A	6: 56,962,583 (GRCm39)	M86K	probably damaging	Het
Vmn2r55	T	A	7: 12,404,830 (GRCm39)	Q191L	possibly damaging	Het
Zfp458	A	T	13: 67,406,012 (GRCm39)	C139*	probably null	Het
Zfp788	T	C	7: 41,299,551 (GRCm39)	L729P	probably damaging	Het
Zmym2	T	A	14: 57,158,102 (GRCm39)	M547K	possibly damaging	Het

Other mutations in Chrd

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01389:Chrd	APN	16	20,559,975 (GRCm39)	missense	possibly damaging	0.89
IGL01486:Chrd	APN	16	20,552,890 (GRCm39)	splice site	probably null
IGL02120:Chrd	APN	16	20,553,291 (GRCm39)	missense	probably damaging	1.00
IGL02370:Chrd	APN	16	20,554,541 (GRCm39)	missense	possibly damaging	0.52
IGL02675:Chrd	APN	16	20,558,699 (GRCm39)	splice site	probably benign
IGL02678:Chrd	APN	16	20,552,770 (GRCm39)	missense	probably damaging	1.00
IGL02874:Chrd	APN	16	20,553,946 (GRCm39)	missense	probably damaging	1.00
ANU74:Chrd	UTSW	16	20,560,069 (GRCm39)	missense	possibly damaging	0.88
PIT1430001:Chrd	UTSW	16	20,557,748 (GRCm39)	critical splice donor site	probably null
R0016:Chrd	UTSW	16	20,553,058 (GRCm39)	missense	possibly damaging	0.85
R0230:Chrd	UTSW	16	20,552,025 (GRCm39)	missense	probably benign	0.25
R0605:Chrd	UTSW	16	20,554,189 (GRCm39)	missense	probably damaging	1.00
R0831:Chrd	UTSW	16	20,560,059 (GRCm39)	missense	probably damaging	0.99
R1501:Chrd	UTSW	16	20,556,283 (GRCm39)	missense	probably damaging	1.00
R1659:Chrd	UTSW	16	20,554,581 (GRCm39)	missense	probably damaging	0.96
R1766:Chrd	UTSW	16	20,556,191 (GRCm39)	missense	probably damaging	1.00
R1823:Chrd	UTSW	16	20,560,097 (GRCm39)	splice site	probably benign
R3001:Chrd	UTSW	16	20,556,195 (GRCm39)	nonsense	probably null
R3002:Chrd	UTSW	16	20,556,195 (GRCm39)	nonsense	probably null
R3874:Chrd	UTSW	16	20,557,660 (GRCm39)	missense	probably damaging	0.99
R4319:Chrd	UTSW	16	20,555,798 (GRCm39)	missense	probably damaging	0.99
R4587:Chrd	UTSW	16	20,557,325 (GRCm39)	missense	possibly damaging	0.58
R4707:Chrd	UTSW	16	20,557,558 (GRCm39)	missense	possibly damaging	0.58
R4857:Chrd	UTSW	16	20,557,508 (GRCm39)	missense	possibly damaging	0.79
R5204:Chrd	UTSW	16	20,554,822 (GRCm39)	missense	probably benign	0.02
R5445:Chrd	UTSW	16	20,557,660 (GRCm39)	missense	possibly damaging	0.74
R5611:Chrd	UTSW	16	20,557,724 (GRCm39)	missense	probably damaging	1.00
R5940:Chrd	UTSW	16	20,553,336 (GRCm39)	missense	probably null	0.01
R6004:Chrd	UTSW	16	20,553,987 (GRCm39)	missense	possibly damaging	0.92
R6767:Chrd	UTSW	16	20,557,376 (GRCm39)	missense	probably benign	0.00
R6798:Chrd	UTSW	16	20,553,056 (GRCm39)	missense	probably damaging	1.00
R6801:Chrd	UTSW	16	20,554,497 (GRCm39)	missense	possibly damaging	0.68
R6823:Chrd	UTSW	16	20,553,486 (GRCm39)	missense	probably damaging	1.00
R6999:Chrd	UTSW	16	20,554,402 (GRCm39)	missense	probably benign
R7069:Chrd	UTSW	16	20,558,183 (GRCm39)	missense	probably damaging	1.00
R7136:Chrd	UTSW	16	20,553,272 (GRCm39)	missense	possibly damaging	0.82
R7273:Chrd	UTSW	16	20,560,316 (GRCm39)	missense	probably benign	0.32
R7558:Chrd	UTSW	16	20,557,304 (GRCm39)	missense	probably damaging	1.00
R7813:Chrd	UTSW	16	20,554,155 (GRCm39)	missense	probably benign	0.00
R7965:Chrd	UTSW	16	20,557,903 (GRCm39)	missense	probably benign	0.05
R8361:Chrd	UTSW	16	20,557,487 (GRCm39)	missense	possibly damaging	0.92
R8549:Chrd	UTSW	16	20,560,027 (GRCm39)	missense	probably benign	0.40
R8809:Chrd	UTSW	16	20,553,270 (GRCm39)	missense	probably benign	0.19
R8841:Chrd	UTSW	16	20,554,487 (GRCm39)	splice site	probably benign
R9027:Chrd	UTSW	16	20,555,737 (GRCm39)	missense	probably damaging	1.00
R9166:Chrd	UTSW	16	20,554,572 (GRCm39)	missense	probably benign	0.28
R9255:Chrd	UTSW	16	20,558,801 (GRCm39)	missense	probably damaging	1.00
R9618:Chrd	UTSW	16	20,552,378 (GRCm39)	missense	probably damaging	1.00
X0063:Chrd	UTSW	16	20,556,314 (GRCm39)	critical splice donor site	probably null
Z1088:Chrd	UTSW	16	20,560,005 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GCACTAAAGTGGAGTACGGC -3'
(R):5'- ACTTGCCAGGAGTCAGACTC -3'

Sequencing Primer
(F):5'- AGTACGGCCCGGGTCAG -3'
(R):5'- AGTCAGACTCCCCTCCCG -3'

Posted On

2016-08-04