Mutagenetix > Incidental Mutation

Incidental Mutation 'R1823:Chrd'

206607

Institutional Source

Beutler Lab

Gene Symbol

Chrd

Ensembl Gene

ENSMUSG00000006958

Gene Name

chordin

Synonyms

Chd

MMRRC Submission

039851-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1823 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

20551877-20561134 bp(+) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

A to G at 20560097 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000156080 (fasta)

Gene Model

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

AlphaFold

Q9Z0E2

Predicted Effect

probably benign
Transcript: ENSMUST00000007171

SMART Domains

Protein: ENSMUSP00000007171
Gene: ENSMUSG00000006958

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

noncoding transcript
Transcript: ENSMUST00000083438

Predicted Effect

probably benign
Transcript: ENSMUST00000115423

SMART Domains

Protein: ENSMUSP00000111083
Gene: ENSMUSG00000006958

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

noncoding transcript
Transcript: ENSMUST00000151150

Predicted Effect

probably benign
Transcript: ENSMUST00000153299

SMART Domains

Protein: ENSMUSP00000138259
Gene: ENSMUSG00000006958

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 benign
Transcript: ENSMUST00000231636

Predicted Effect

probably benign
Transcript: ENSMUST00000231698

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232104

Predicted Effect

probably benign
Transcript: ENSMUST00000232646

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 95.1%
20x: 91.6%

Validation Efficiency

98% (87/89)

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: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adcy1	G	A	11: 7,111,312 (GRCm39)	V868I	probably benign	Het
Ahnak	G	T	19: 8,982,269 (GRCm39)	M1184I	probably damaging	Het
Akap11	T	C	14: 78,748,928 (GRCm39)	E1153G	probably damaging	Het
Amy1	T	C	3: 113,356,376 (GRCm39)	N260S	probably null	Het
Ankrd6	A	G	4: 32,824,427 (GRCm39)	L129P	probably damaging	Het
Aox1	A	T	1: 58,351,518 (GRCm39)	T702S	probably benign	Het
Apobec1	G	T	6: 122,555,845 (GRCm39)	T204K	possibly damaging	Het
Arhgef19	A	G	4: 140,976,457 (GRCm39)	R433G	probably benign	Het
Atf6b	T	A	17: 34,867,618 (GRCm39)	H110Q	possibly damaging	Het
Btnl4	C	T	17: 34,694,826 (GRCm39)		probably null	Het
Camsap2	T	C	1: 136,201,521 (GRCm39)	T662A	possibly damaging	Het
Cbs	G	A	17: 31,843,245 (GRCm39)	H229Y	probably damaging	Het
Cct8	G	A	16: 87,287,442 (GRCm39)	R111*	probably null	Het
Cdc42bpb	C	T	12: 111,293,993 (GRCm39)	A250T	probably damaging	Het
Ckap2l	A	G	2: 129,117,499 (GRCm39)	F559L	probably damaging	Het
Cltrn	A	G	X: 162,901,230 (GRCm39)	D184G	possibly damaging	Het
D630003M21Rik	T	C	2: 158,059,477 (GRCm39)	Y141C	probably damaging	Het
Dbf4	T	C	5: 8,447,539 (GRCm39)	N557S	probably benign	Het
Dct	T	G	14: 118,273,935 (GRCm39)	N324T	probably benign	Het
Dip2a	A	T	10: 76,114,336 (GRCm39)	L999*	probably null	Het
Dock10	T	A	1: 80,520,814 (GRCm39)		probably null	Het
Dync2li1	A	T	17: 84,957,225 (GRCm39)	D330V	probably damaging	Het
Eif4g3	T	A	4: 137,907,802 (GRCm39)	D1267E	probably benign	Het
Enc1	A	G	13: 97,382,486 (GRCm39)	E332G	possibly damaging	Het
Fat2	C	T	11: 55,147,606 (GRCm39)	V3879I	probably benign	Het
Fh1	A	T	1: 175,444,114 (GRCm39)	I117K	probably damaging	Het
Fkbp15	A	G	4: 62,255,328 (GRCm39)	L227P	probably damaging	Het
Fpr1	T	A	17: 18,097,315 (GRCm39)	M225L	probably benign	Het
Fras1	A	T	5: 96,918,547 (GRCm39)	I3528F	probably damaging	Het
Grm7	A	G	6: 111,184,730 (GRCm39)	T354A	probably benign	Het
Ift27	T	A	15: 78,057,978 (GRCm39)	I9F	possibly damaging	Het
Igf1r	A	G	7: 67,844,729 (GRCm39)	D834G	possibly damaging	Het
Igsf9b	T	A	9: 27,243,028 (GRCm39)	L738Q	probably damaging	Het
Itgam	A	T	7: 127,663,904 (GRCm39)	T44S	probably benign	Het
Ivd	T	A	2: 118,692,515 (GRCm39)	I5N	probably benign	Het
Jcad	T	C	18: 4,675,780 (GRCm39)	S1181P	probably damaging	Het
Kctd18	A	G	1: 57,995,524 (GRCm39)	V251A	probably benign	Het
Mycbp2	A	G	14: 103,489,945 (GRCm39)	V953A	possibly damaging	Het
Myo18a	T	C	11: 77,715,923 (GRCm39)		probably benign	Het
Myo3a	A	T	2: 22,345,091 (GRCm39)	Y509F	probably damaging	Het
Myocd	C	A	11: 65,069,496 (GRCm39)	M909I	probably benign	Het
Ndufv3	G	A	17: 31,750,219 (GRCm39)	R467Q	probably damaging	Het
Nkpd1	G	A	7: 19,257,177 (GRCm39)	V319M	probably damaging	Het
Or13p4	T	A	4: 118,547,389 (GRCm39)	N87Y	probably damaging	Het
Or1af1	T	C	2: 37,110,344 (GRCm39)	V281A	probably damaging	Het
Or1p1c	C	T	11: 74,161,043 (GRCm39)	A276V	probably damaging	Het
Or2q1	G	T	6: 42,795,202 (GRCm39)	A266S	possibly damaging	Het
Or2t1	T	A	14: 14,328,774 (GRCm38)	L221Q	probably damaging	Het
Or4c111	A	G	2: 88,843,722 (GRCm39)	S229P	probably benign	Het
Or5b101	C	A	19: 13,005,181 (GRCm39)	V171L	probably benign	Het
Parp4	T	C	14: 56,827,329 (GRCm39)		probably benign	Het
Pcdhb9	A	G	18: 37,535,871 (GRCm39)	T622A	probably benign	Het
Pdpk1	A	T	17: 24,317,150 (GRCm39)		probably benign	Het
Pkhd1	C	A	1: 20,417,681 (GRCm39)	G2490V	probably damaging	Het
Plekhg1	G	T	10: 3,853,658 (GRCm39)		probably null	Het
Plekhh2	A	G	17: 84,882,617 (GRCm39)	Y708C	probably damaging	Het
Pnp	T	C	14: 51,187,786 (GRCm39)	F107L	probably damaging	Het
Postn	T	A	3: 54,292,708 (GRCm39)		probably null	Het
Prcp	A	T	7: 92,577,883 (GRCm39)	D349V	probably damaging	Het
Prl3a1	A	T	13: 27,454,177 (GRCm39)	I52F	probably damaging	Het
Pym1	G	A	10: 128,601,913 (GRCm39)		probably benign	Het
Rad9a	A	T	19: 4,247,241 (GRCm39)	I248N	probably damaging	Het
Ror2	T	G	13: 53,264,341 (GRCm39)	E917A	probably benign	Het
Rsf1	G	A	7: 97,229,117 (GRCm39)		probably benign	Het
Sema6d	A	G	2: 124,501,476 (GRCm39)		probably null	Het
Shisal1	T	C	15: 84,290,669 (GRCm39)	T213A	probably benign	Het
Slc4a2	C	T	5: 24,632,618 (GRCm39)	A12V	probably damaging	Het
Slco6b1	T	G	1: 96,888,901 (GRCm39)		noncoding transcript	Het
Slf2	A	T	19: 44,923,687 (GRCm39)	H167L	possibly damaging	Het
Snx9	G	T	17: 5,970,946 (GRCm39)	G429V	probably damaging	Het
Sod3	G	T	5: 52,525,504 (GRCm39)	V68L	probably benign	Het
Spta1	T	A	1: 174,074,115 (GRCm39)	D2351E	probably benign	Het
Srpk3	G	A	X: 72,821,561 (GRCm39)	R425Q	possibly damaging	Het
Tatdn1	C	T	15: 58,788,005 (GRCm39)	G171E	probably damaging	Het
Tbc1d22a	T	C	15: 86,119,770 (GRCm39)	V22A	possibly damaging	Het
Tnfsf9	A	G	17: 57,412,738 (GRCm39)	T103A	probably benign	Het
Tpm3-rs7	T	C	14: 113,552,595 (GRCm39)	L163P	possibly damaging	Het
Trim52	T	A	14: 106,344,401 (GRCm39)	C20S	probably damaging	Het
Ucp1	C	T	8: 84,020,661 (GRCm39)	T157I	probably damaging	Het
Uspl1	T	A	5: 149,151,224 (GRCm39)	L794Q	probably benign	Het
Vmn1r5	T	A	6: 56,962,580 (GRCm39)	V85E	probably damaging	Het
Vmn1r58	A	G	7: 5,413,405 (GRCm39)	I275T	possibly damaging	Het
Vmn2r79	A	G	7: 86,687,080 (GRCm39)	I820M	probably damaging	Het
Wscd1	C	A	11: 71,651,044 (GRCm39)	P124T	probably benign	Het
Zfp780b	A	T	7: 27,662,525 (GRCm39)	C677S	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
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
R5364:Chrd	UTSW	16	20,551,898 (GRCm39)	start codon destroyed	probably null	0.03
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'- AAACTACTAGGCTAGGGGAATTC -3'
(R):5'- TGAACAATCGTCCCGCTCAC -3'

Sequencing Primer
(F):5'- AGTTGGTTGACCCTTATTGTCTAAC -3'
(R):5'- CCGCTCACAGTGGGGTAC -3'

Posted On

2014-06-23