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

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R7069 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

20733127-20742384 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 20739433 bp (GRCm38)

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
2010300C02Rik	A	T	1: 37,631,901	F97Y	probably damaging	Het
4932415D10Rik	G	A	10: 82,289,943	T2411I	probably damaging	Het
Aasdh	T	A	5: 76,876,356	I991L	probably benign	Het
Actg2	C	A	6: 83,520,763	G96V	probably damaging	Het
Adh5	T	A	3: 138,451,051	L166*	probably null	Het
Akap13	A	G	7: 75,610,262	D75G	probably benign	Het
Ank2	T	C	3: 126,946,298		probably benign	Het
Arfgap1	T	A	2: 180,974,120	D197E	probably benign	Het
Aste1	T	C	9: 105,396,707		probably null	Het
Atp8b2	T	A	3: 89,954,571	N78I	probably damaging	Het
Btbd11	C	A	10: 85,387,656	R110S	unknown	Het
Cacna2d3	T	A	14: 28,969,303		probably benign	Het
Col2a1	C	T	15: 97,998,588	G60D	unknown	Het
Coro7	T	A	16: 4,679,611	M1L	probably damaging	Het
Dhx40	T	C	11: 86,797,743	I285V	probably benign	Het
Dopey1	T	C	9: 86,550,169		probably null	Het
Enox1	A	T	14: 77,611,324	R358S	probably damaging	Het
Ep400	A	G	5: 110,668,124	V2724A	probably damaging	Het
Fam196b	T	A	11: 34,402,677	C240S	possibly damaging	Het
Fam221a	A	C	6: 49,378,498	Q178P	probably damaging	Het
Fcho1	A	C	8: 71,710,497		probably null	Het
Fndc1	A	T	17: 7,769,735	V1165D	unknown	Het
Gal3st2b	A	T	1: 93,940,619	N189Y	possibly damaging	Het
Ghr	T	A	15: 3,320,484	D404V	probably damaging	Het
Glis3	A	T	19: 28,531,519	V355D	probably damaging	Het
Gm15922	C	G	7: 3,737,320	A301P	probably damaging	Het
Gm21671	A	T	5: 25,949,844	S253T	possibly damaging	Het
Gpr12	A	C	5: 146,583,539	V32G	possibly damaging	Het
Gspt1	T	A	16: 11,222,661	L593F	probably damaging	Het
H2-Q7	A	T	17: 35,440,031	T153S	probably damaging	Het
Hars2	A	G	18: 36,787,956	I194V	probably damaging	Het
Hdac9	T	A	12: 34,429,549	T202S	possibly damaging	Het
Hoxd13	T	C	2: 74,669,024	Y239H	probably damaging	Het
Insm2	C	T	12: 55,599,836	Q122*	probably null	Het
Ip6k1	T	A	9: 108,045,452		probably null	Het
Ippk	T	C	13: 49,461,743	V534A	probably damaging	Het
Itch	T	G	2: 155,209,994	F611C	probably damaging	Het
Itga1	A	T	13: 114,968,240	N1083K	probably damaging	Het
Itgae	A	C	11: 73,116,143	D405A	probably damaging	Het
Kif18a	T	C	2: 109,295,002	S255P	probably damaging	Het
Klhl24	C	G	16: 20,107,481	T253R	probably benign	Het
Krt81	T	A	15: 101,460,728	T307S	possibly damaging	Het
Lbr	A	T	1: 181,828,789	W265R	probably damaging	Het
Lgals3bp	T	C	11: 118,393,173	T527A	probably benign	Het
Lzts1	A	C	8: 69,140,745	V70G	probably damaging	Het
Map3k6	C	T	4: 133,251,712	P1154S	probably benign	Het
Masp1	T	C	16: 23,452,455	D681G	probably benign	Het
Mdga2	T	C	12: 66,486,752	N948D	probably benign	Het
Mettl4	A	T	17: 94,733,633	F364L	probably damaging	Het
Mosmo	T	C	7: 120,677,832	I23T	probably benign	Het
Mtg1	G	A	7: 140,143,744	V96I	probably benign	Het
Myh11	T	A	16: 14,218,939	R966S	possibly damaging	Het
Ncapg2	A	G	12: 116,424,717		probably null	Het
Nid1	G	A	13: 13,508,768	V1144I	probably benign	Het
Olfr1250	T	C	2: 89,656,566	I292V	probably benign	Het
Olfr544	C	A	7: 102,484,772	C116F	possibly damaging	Het
Olfr622	A	T	7: 103,639,960	M60K	probably damaging	Het
Oscar	T	G	7: 3,611,239	Y167S	probably damaging	Het
Pa2g4	T	C	10: 128,560,690	T200A	probably benign	Het
Pcdh7	A	G	5: 57,719,784	D227G	probably benign	Het
Plce1	G	A	19: 38,758,940	G1702R	probably damaging	Het
Plxna2	C	A	1: 194,793,904	T1144K	possibly damaging	Het
Prl8a8	G	A	13: 27,511,467	T99I	probably benign	Het
Prr29	C	A	11: 106,376,259	H83Q	probably damaging	Het
Raly	T	A	2: 154,859,744	I108N	possibly damaging	Het
Ranbp9	A	T	13: 43,419,622	S475R	probably benign	Het
Rogdi	C	A	16: 5,013,498		probably benign	Het
Rorc	C	T	3: 94,372,907	Q6*	probably null	Het
Sacs	T	C	14: 61,212,496	L3997S	probably damaging	Het
Scn2a	A	T	2: 65,764,606	Y1933F	probably benign	Het
Sik3	T	C	9: 46,210,743	L898P	probably damaging	Het
Sipa1l1	A	G	12: 82,341,406	I135M	probably damaging	Het
Slc26a3	C	A	12: 31,450,935	Q224K	probably damaging	Het
Sobp	G	T	10: 43,021,440	N716K	probably benign	Het
Spata16	A	G	3: 26,927,334	D513G	probably damaging	Het
Stac	T	C	9: 111,572,326	R351G	possibly damaging	Het
Tecta	T	A	9: 42,394,941	T64S	probably benign	Het
Tert	G	A	13: 73,628,410	V427M	probably damaging	Het
Tex15	G	A	8: 33,570,720	M333I	probably benign	Het
Tmbim4	A	T	10: 120,220,759	Q72L	probably benign	Het
Trav9n-4	T	C	14: 53,294,799	S37P	probably benign	Het
Trpv5	A	T	6: 41,675,960	M93K	possibly damaging	Het
Ulk4	T	C	9: 121,258,810	E272G	probably benign	Het
Ulk4	T	C	9: 121,266,517	T79A	probably benign	Het
Upb1	A	G	10: 75,412,768	N41D	probably benign	Het
Wls	A	T	3: 159,934,329	Y532F	probably damaging	Het
Zdhhc5	G	A	2: 84,715,011		probably benign	Het
Zfp109	T	C	7: 24,229,360	D216G	probably benign	Het
Zfp473	G	A	7: 44,732,374	A845V	probably damaging	Het

Other mutations in Chrd

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01389:Chrd	APN	16	20741225	missense	possibly damaging	0.89
IGL01486:Chrd	APN	16	20734140	splice site	probably null
IGL02120:Chrd	APN	16	20734541	missense	probably damaging	1.00
IGL02370:Chrd	APN	16	20735791	missense	possibly damaging	0.52
IGL02675:Chrd	APN	16	20739949	splice site	probably benign
IGL02678:Chrd	APN	16	20734020	missense	probably damaging	1.00
IGL02874:Chrd	APN	16	20735196	missense	probably damaging	1.00
ANU74:Chrd	UTSW	16	20741319	missense	possibly damaging	0.88
PIT1430001:Chrd	UTSW	16	20738998	critical splice donor site	probably null
R0016:Chrd	UTSW	16	20734308	missense	possibly damaging	0.85
R0230:Chrd	UTSW	16	20733275	missense	probably benign	0.25
R0605:Chrd	UTSW	16	20735439	missense	probably damaging	1.00
R0831:Chrd	UTSW	16	20741309	missense	probably damaging	0.99
R1501:Chrd	UTSW	16	20737533	missense	probably damaging	1.00
R1659:Chrd	UTSW	16	20735831	missense	probably damaging	0.96
R1766:Chrd	UTSW	16	20737441	missense	probably damaging	1.00
R1823:Chrd	UTSW	16	20741347	splice site	probably benign
R3001:Chrd	UTSW	16	20737445	nonsense	probably null
R3002:Chrd	UTSW	16	20737445	nonsense	probably null
R3874:Chrd	UTSW	16	20738910	missense	probably damaging	0.99
R4319:Chrd	UTSW	16	20737048	missense	probably damaging	0.99
R4587:Chrd	UTSW	16	20738575	missense	possibly damaging	0.58
R4707:Chrd	UTSW	16	20738808	missense	possibly damaging	0.58
R4857:Chrd	UTSW	16	20738758	missense	possibly damaging	0.79
R5204:Chrd	UTSW	16	20736072	missense	probably benign	0.02
R5364:Chrd	UTSW	16	20733148	start codon destroyed	probably null	0.03
R5445:Chrd	UTSW	16	20738910	missense	possibly damaging	0.74
R5611:Chrd	UTSW	16	20738974	missense	probably damaging	1.00
R5940:Chrd	UTSW	16	20734586	missense	probably null	0.01
R6004:Chrd	UTSW	16	20735237	missense	possibly damaging	0.92
R6767:Chrd	UTSW	16	20738626	missense	probably benign	0.00
R6798:Chrd	UTSW	16	20734306	missense	probably damaging	1.00
R6801:Chrd	UTSW	16	20735747	missense	possibly damaging	0.68
R6823:Chrd	UTSW	16	20734736	missense	probably damaging	1.00
R6999:Chrd	UTSW	16	20735652	missense	probably benign
R7136:Chrd	UTSW	16	20734522	missense	possibly damaging	0.82
R7273:Chrd	UTSW	16	20741566	missense	probably benign	0.32
R7558:Chrd	UTSW	16	20738554	missense	probably damaging	1.00
R7813:Chrd	UTSW	16	20735405	missense	probably benign	0.00
R7965:Chrd	UTSW	16	20739153	missense	probably benign	0.05
R8361:Chrd	UTSW	16	20738737	missense	possibly damaging	0.92
R8549:Chrd	UTSW	16	20741277	missense	probably benign	0.40
R8809:Chrd	UTSW	16	20734520	missense	probably benign	0.19
R8841:Chrd	UTSW	16	20735737	splice site	probably benign
R9027:Chrd	UTSW	16	20736987	missense	probably damaging	1.00
R9166:Chrd	UTSW	16	20735822	missense	probably benign	0.28
R9255:Chrd	UTSW	16	20740051	missense	probably damaging	1.00
R9618:Chrd	UTSW	16	20733628	missense	probably damaging	1.00
X0063:Chrd	UTSW	16	20737564	critical splice donor site	probably null
Z1088:Chrd	UTSW	16	20741255	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