Mutagenetix > Incidental Mutation

Incidental Mutation 'R5940:Chrd'

462528

Institutional Source

Beutler Lab

Gene Symbol

Chrd

Ensembl Gene

ENSMUSG00000006958

Gene Name

chordin

Synonyms

Chd

MMRRC Submission

044132-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5940 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

20733127-20742384 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 20734586 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Leucine at position 226 (R226L)

Ref Sequence

ENSEMBL: ENSMUSP00000156080 (fasta)

Gene Model

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

AlphaFold

Q9Z0E2

Predicted Effect

probably null
Transcript: ENSMUST00000007171
AA Change: R204L

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000007171
Gene: ENSMUSG00000006958
AA Change: R204L

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 null
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: R204L

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000111083
Gene: ENSMUSG00000006958
AA Change: R204L

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 null
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 benign
Transcript: ENSMUST00000153299
AA Change: R204L

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000138259
Gene: ENSMUSG00000006958
AA Change: R204L

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
AA Change: R204L

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000231689

Predicted Effect

probably benign
Transcript: ENSMUST00000231698
AA Change: R226L

PolyPhen 2 Score 0.039 (Sensitivity: 0.94; Specificity: 0.83)

Predicted Effect

probably null
Transcript: ENSMUST00000231826

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232020

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232104

Predicted Effect

probably null
Transcript: ENSMUST00000232217

Predicted Effect

probably null
Transcript: ENSMUST00000232646
AA Change: R226L

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)

Meta Mutation Damage Score

0.5252

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.2%
20x: 95.0%

Validation Efficiency

96% (88/92)

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: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610037L13Rik	A	G	4: 107,893,288		probably benign	Het
1110008L16Rik	T	A	12: 55,304,874	W323R	probably damaging	Het
1500015O10Rik	C	T	1: 43,737,241	R41*	probably null	Het
3425401B19Rik	T	C	14: 32,662,688	Y440C	possibly damaging	Het
5430419D17Rik	A	T	7: 131,238,263	D638V	probably damaging	Het
Aasdh	G	T	5: 76,882,898	S618R	probably benign	Het
Alpk1	T	G	3: 127,670,946	T1228P	probably benign	Het
Ank3	T	C	10: 69,920,486	V850A	probably benign	Het
Apeh	A	T	9: 108,091,899		probably null	Het
Ash1l	C	T	3: 88,984,036	T1074I	probably damaging	Het
C3	G	A	17: 57,210,244	S1297F	possibly damaging	Het
Cchcr1	G	A	17: 35,524,993	R284Q	probably damaging	Het
Cd93	A	T	2: 148,442,232	I398N	probably benign	Het
Clvs1	A	T	4: 9,449,443	N344I	possibly damaging	Het
Cyp4v3	A	T	8: 45,321,784	I111N	probably damaging	Het
Cysltr2	T	C	14: 73,029,491	K260E	probably benign	Het
Cysltr2	T	A	14: 73,029,949	Y107F	probably damaging	Het
Defb47	A	T	14: 63,000,910	E28D	probably benign	Het
Dnajc30	T	A	5: 135,064,559	Y103*	probably null	Het
Drap1	T	C	19: 5,423,000	T160A	probably benign	Het
Dsp	A	G	13: 38,196,026	E2249G	possibly damaging	Het
E2f8	T	A	7: 48,871,077	I499F	probably benign	Het
Ebf1	T	A	11: 44,621,221	Y116N	probably damaging	Het
Ect2	C	A	3: 27,115,465	E746D	probably benign	Het
Enpep	T	A	3: 129,312,578	Y333F	probably damaging	Het
Fat4	T	C	3: 38,889,649	V897A	probably benign	Het
Gja3	T	A	14: 57,035,860	S352C	probably damaging	Het
Gm884	T	C	11: 103,613,886	S243G	probably benign	Het
Gpr153	C	A	4: 152,283,375	P561Q	probably benign	Het
Hlcs	T	C	16: 94,134,712	M574V	probably damaging	Het
Hmcn1	A	G	1: 150,657,222	V3070A	probably benign	Het
Hsd3b2	G	T	3: 98,711,971	N219K	probably benign	Het
Htra3	T	C	5: 35,652,980	I453V	possibly damaging	Het
Klrc1	A	T	6: 129,674,935	M220K	possibly damaging	Het
Kntc1	T	G	5: 123,786,195	I1048S	probably benign	Het
Macf1	T	A	4: 123,432,881	D2822V	probably damaging	Het
Mcu	T	A	10: 59,456,732	I42F	possibly damaging	Het
Mkln1	T	A	6: 31,489,372	D521E	probably damaging	Het
Ms4a13	T	C	19: 11,192,966	N5D	possibly damaging	Het
Msh3	T	G	13: 92,249,843	N838T	probably damaging	Het
Msl2	T	A	9: 101,101,091	C221*	probably null	Het
Ncapd2	A	G	6: 125,168,869	S1310P	probably benign	Het
Ncoa6	A	T	2: 155,415,865	M586K	probably damaging	Het
Ndel1	C	T	11: 68,822,571		probably benign	Het
Ndst4	T	C	3: 125,561,419		probably benign	Het
Nes	T	G	3: 87,975,952	V506G	probably damaging	Het
Nrg1	T	C	8: 31,849,344	K200E	probably damaging	Het
Nt5c1b	A	G	12: 10,375,515	K295E	probably damaging	Het
Olfr1085	A	T	2: 86,658,050	M136K	probably damaging	Het
Olfr1278	G	A	2: 111,292,384	V39M	possibly damaging	Het
Olfr1487	T	A	19: 13,619,153		probably null	Het
Olfr750	T	A	14: 51,070,722	I224L	probably damaging	Het
Olfr878	C	T	9: 37,919,437	T260I	probably damaging	Het
Olfr919	G	T	9: 38,697,711	Y218*	probably null	Het
Otx1	C	A	11: 21,997,037	A91S	probably damaging	Het
Pde1a	A	G	2: 79,887,839		probably null	Het
Pds5a	A	G	5: 65,643,985		probably benign	Het
Plbd1	A	T	6: 136,613,721		probably benign	Het
Plod2	T	A	9: 92,591,397	V292E	probably benign	Het
Polg	A	G	7: 79,454,071	V879A	possibly damaging	Het
Ppargc1a	C	T	5: 51,473,911	A459T	probably damaging	Het
Psip1	T	C	4: 83,476,322	E83G	probably damaging	Het
Rhbdf1	T	C	11: 32,209,847	D843G	probably benign	Het
Rnpepl1	G	T	1: 92,917,712	C451F	probably damaging	Het
Rrp1	T	C	10: 78,405,415	D206G	probably damaging	Het
Setbp1	A	T	18: 78,755,488	D1492E	probably damaging	Het
Sh3bp5	C	A	14: 31,377,495	R265L	probably benign	Het
Slc16a6	C	T	11: 109,473,196		probably benign	Homo
Slc7a6os	A	G	8: 106,210,805	S37P	probably damaging	Het
Tenm4	T	A	7: 96,845,895	S1140T	probably damaging	Het
Thoc6	C	A	17: 23,670,341	R115L	probably benign	Het
Tmem63c	C	T	12: 87,075,172	H385Y	probably benign	Het
Trpm8	G	T	1: 88,351,415	E649*	probably null	Het
Usf1	A	G	1: 171,417,779	E253G	possibly damaging	Het
Vps13d	T	C	4: 145,074,975	T443A	probably benign	Het
Wdr86	T	C	5: 24,722,662	Y93C	probably damaging	Het
Zfp597	A	T	16: 3,865,821	I357N	probably damaging	Het
Zfp709	A	G	8: 71,890,220	I497V	possibly damaging	Het
Zxdc	T	C	6: 90,370,325	S223P	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
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
R7069:Chrd	UTSW	16	20739433	missense	probably damaging	1.00
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'- CAGTTACAGTGATCGAGGGG -3'
(R):5'- TTGCAGGGTGTTCAAACAGG -3'

Sequencing Primer
(F):5'- TGCTGATGGCCACACAGGTAG -3'
(R):5'- GTGTTCAAACAGGATGTTGCC -3'

Posted On

2017-02-28