Mutagenetix > Incidental Mutation

Incidental Mutation 'R7069:Chrd'

548797

Institutional Source

Beutler Lab

Gene Symbol

Chrd

Ensembl Gene

ENSMUSG00000006958

Gene Name

chordin

Synonyms

Chd

MMRRC Submission

045165-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7069 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

20551877-20561134 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 20558183 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tryptophan to Arginine at position 809 (W809R)

Ref Sequence

ENSEMBL: ENSMUSP00000156080 (fasta)

Gene Model

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

AlphaFold

Q9Z0E2

Predicted Effect

probably damaging
Transcript: ENSMUST00000007171
AA Change: W787R

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

SMART Domains

Protein: ENSMUSP00000007171
Gene: ENSMUSG00000006958
AA Change: W787R

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: 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

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

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

probably damaging
Transcript: ENSMUST00000232646
AA Change: W809R

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

98% (86/88)

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: 89 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aasdh	T	A	5: 77,024,203 (GRCm39)	I991L	probably benign	Het
Abtb3	C	A	10: 85,223,520 (GRCm39)	R110S	unknown	Het
Actg2	C	A	6: 83,497,745 (GRCm39)	G96V	probably damaging	Het
Adh5	T	A	3: 138,156,812 (GRCm39)	L166*	probably null	Het
Akap13	A	G	7: 75,260,010 (GRCm39)	D75G	probably benign	Het
Ank2	T	C	3: 126,739,947 (GRCm39)		probably benign	Het
Arfgap1	T	A	2: 180,615,913 (GRCm39)	D197E	probably benign	Het
Aste1	T	C	9: 105,273,906 (GRCm39)		probably null	Het
Atp8b2	T	A	3: 89,861,878 (GRCm39)	N78I	probably damaging	Het
Cacna2d3	T	A	14: 28,691,260 (GRCm39)		probably benign	Het
Col2a1	C	T	15: 97,896,469 (GRCm39)	G60D	unknown	Het
Coro7	T	A	16: 4,497,475 (GRCm39)	M1L	probably damaging	Het
Cracdl	A	T	1: 37,670,982 (GRCm39)	F97Y	probably damaging	Het
Dhx40	T	C	11: 86,688,569 (GRCm39)	I285V	probably benign	Het
Dop1a	T	C	9: 86,432,222 (GRCm39)		probably null	Het
Enox1	A	T	14: 77,848,764 (GRCm39)	R358S	probably damaging	Het
Ep400	A	G	5: 110,815,990 (GRCm39)	V2724A	probably damaging	Het
Fam221a	A	C	6: 49,355,432 (GRCm39)	Q178P	probably damaging	Het
Fcho1	A	C	8: 72,163,141 (GRCm39)		probably null	Het
Fndc1	A	T	17: 7,988,567 (GRCm39)	V1165D	unknown	Het
Gal3st2b	A	T	1: 93,868,341 (GRCm39)	N189Y	possibly damaging	Het
Ghr	T	A	15: 3,349,966 (GRCm39)	D404V	probably damaging	Het
Glis3	A	T	19: 28,508,919 (GRCm39)	V355D	probably damaging	Het
Gpr12	A	C	5: 146,520,349 (GRCm39)	V32G	possibly damaging	Het
Gspt1	T	A	16: 11,040,525 (GRCm39)	L593F	probably damaging	Het
H2-Q7	A	T	17: 35,659,007 (GRCm39)	T153S	probably damaging	Het
Hars2	A	G	18: 36,921,009 (GRCm39)	I194V	probably damaging	Het
Hdac9	T	A	12: 34,479,548 (GRCm39)	T202S	possibly damaging	Het
Hoxd13	T	C	2: 74,499,368 (GRCm39)	Y239H	probably damaging	Het
Insm2	C	T	12: 55,646,621 (GRCm39)	Q122*	probably null	Het
Insyn2b	T	A	11: 34,352,677 (GRCm39)	C240S	possibly damaging	Het
Ip6k1	T	A	9: 107,922,651 (GRCm39)		probably null	Het
Ippk	T	C	13: 49,615,219 (GRCm39)	V534A	probably damaging	Het
Itch	T	G	2: 155,051,914 (GRCm39)	F611C	probably damaging	Het
Itga1	A	T	13: 115,104,776 (GRCm39)	N1083K	probably damaging	Het
Itgae	A	C	11: 73,006,969 (GRCm39)	D405A	probably damaging	Het
Kif18a	T	C	2: 109,125,347 (GRCm39)	S255P	probably damaging	Het
Klhl24	C	G	16: 19,926,231 (GRCm39)	T253R	probably benign	Het
Krt81	T	A	15: 101,358,609 (GRCm39)	T307S	possibly damaging	Het
Lbr	A	T	1: 181,656,354 (GRCm39)	W265R	probably damaging	Het
Lgals3bp	T	C	11: 118,283,999 (GRCm39)	T527A	probably benign	Het
Lzts1	A	C	8: 69,593,397 (GRCm39)	V70G	probably damaging	Het
Map3k6	C	T	4: 132,979,023 (GRCm39)	P1154S	probably benign	Het
Masp1	T	C	16: 23,271,205 (GRCm39)	D681G	probably benign	Het
Mdga2	T	C	12: 66,533,526 (GRCm39)	N948D	probably benign	Het
Mettl4	A	T	17: 95,041,061 (GRCm39)	F364L	probably damaging	Het
Mosmo	T	C	7: 120,277,055 (GRCm39)	I23T	probably benign	Het
Mtg1	G	A	7: 139,723,657 (GRCm39)	V96I	probably benign	Het
Myh11	T	A	16: 14,036,803 (GRCm39)	R966S	possibly damaging	Het
Ncapg2	A	G	12: 116,388,337 (GRCm39)		probably null	Het
Nid1	G	A	13: 13,683,353 (GRCm39)	V1144I	probably benign	Het
Or4a77	T	C	2: 89,486,910 (GRCm39)	I292V	probably benign	Het
Or52a33	A	T	7: 103,289,167 (GRCm39)	M60K	probably damaging	Het
Or55b4	C	A	7: 102,133,979 (GRCm39)	C116F	possibly damaging	Het
Oscar	T	G	7: 3,614,238 (GRCm39)	Y167S	probably damaging	Het
Pa2g4	T	C	10: 128,396,559 (GRCm39)	T200A	probably benign	Het
Pcdh7	A	G	5: 57,877,126 (GRCm39)	D227G	probably benign	Het
Pira1	C	G	7: 3,740,319 (GRCm39)	A301P	probably damaging	Het
Plce1	G	A	19: 38,747,384 (GRCm39)	G1702R	probably damaging	Het
Plxna2	C	A	1: 194,476,212 (GRCm39)	T1144K	possibly damaging	Het
Prl8a8	G	A	13: 27,695,450 (GRCm39)	T99I	probably benign	Het
Prr29	C	A	11: 106,267,085 (GRCm39)	H83Q	probably damaging	Het
Raly	T	A	2: 154,701,664 (GRCm39)	I108N	possibly damaging	Het
Ranbp9	A	T	13: 43,573,098 (GRCm39)	S475R	probably benign	Het
Rogdi	C	A	16: 4,831,362 (GRCm39)		probably benign	Het
Rorc	C	T	3: 94,280,214 (GRCm39)	Q6*	probably null	Het
Sacs	T	C	14: 61,449,945 (GRCm39)	L3997S	probably damaging	Het
Scn2a	A	T	2: 65,594,950 (GRCm39)	Y1933F	probably benign	Het
Sik3	T	C	9: 46,122,041 (GRCm39)	L898P	probably damaging	Het
Sipa1l1	A	G	12: 82,388,180 (GRCm39)	I135M	probably damaging	Het
Slc26a3	C	A	12: 31,500,934 (GRCm39)	Q224K	probably damaging	Het
Sobp	G	T	10: 42,897,436 (GRCm39)	N716K	probably benign	Het
Spata16	A	G	3: 26,981,483 (GRCm39)	D513G	probably damaging	Het
Spata31h1	G	A	10: 82,125,777 (GRCm39)	T2411I	probably damaging	Het
Speer4a3	A	T	5: 26,154,842 (GRCm39)	S253T	possibly damaging	Het
Stac	T	C	9: 111,401,394 (GRCm39)	R351G	possibly damaging	Het
Tecta	T	A	9: 42,306,237 (GRCm39)	T64S	probably benign	Het
Tert	G	A	13: 73,776,529 (GRCm39)	V427M	probably damaging	Het
Tex15	G	A	8: 34,060,748 (GRCm39)	M333I	probably benign	Het
Tmbim4	A	T	10: 120,056,664 (GRCm39)	Q72L	probably benign	Het
Trav9n-4	T	C	14: 53,532,256 (GRCm39)	S37P	probably benign	Het
Trpv5	A	T	6: 41,652,894 (GRCm39)	M93K	possibly damaging	Het
Ulk4	T	C	9: 121,087,876 (GRCm39)	E272G	probably benign	Het
Ulk4	T	C	9: 121,095,583 (GRCm39)	T79A	probably benign	Het
Upb1	A	G	10: 75,248,602 (GRCm39)	N41D	probably benign	Het
Wls	A	T	3: 159,639,965 (GRCm39)	Y532F	probably damaging	Het
Zdhhc5	G	A	2: 84,545,355 (GRCm39)		probably benign	Het
Zfp109	T	C	7: 23,928,785 (GRCm39)	D216G	probably benign	Het
Zfp473	G	A	7: 44,381,798 (GRCm39)	A845V	probably 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
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
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'- CAAAGAAGCCATTGGGTTGG -3'
(R):5'- ATCAAGGACAGGCTTGCTCTC -3'

Sequencing Primer
(F):5'- GAAGCTGAGGTGCACAGACTC -3'
(R):5'- TGCTCTCCAGGAAGTCCC -3'

Posted On

2019-05-13