Mutagenetix > Incidental Mutation

Incidental Mutation 'R6999:Chrd'

544418

Institutional Source

Beutler Lab

Gene Symbol

Chrd

Ensembl Gene

ENSMUSG00000006958

Gene Name

chordin

Synonyms

Chd

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6999 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

20733127-20742384 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 20735652 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 370 (T370A)

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 benign
Transcript: ENSMUST00000007171
AA Change: T348A

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

SMART Domains

Protein: ENSMUSP00000007171
Gene: ENSMUSG00000006958
AA Change: T348A

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
AA Change: T348A

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

SMART Domains

Protein: ENSMUSP00000111083
Gene: ENSMUSG00000006958
AA Change: T348A

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 benign
Transcript: ENSMUST00000232646
AA Change: T370A

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.0%

Validation Efficiency

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: 57 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca12	G	A	1: 71,317,162	Q629*	probably null	Het
Acss3	C	A	10: 107,053,501	G153C	probably damaging	Het
Alpk2	A	G	18: 65,304,513	S1270P	probably damaging	Het
Ankrd10	A	T	8: 11,619,106	L215Q	probably damaging	Het
Ankrd6	A	G	4: 32,823,459	S188P	probably benign	Het
Brinp2	A	G	1: 158,251,305	M316T	probably benign	Het
Bsn	A	G	9: 108,113,433	S1707P	probably benign	Het
C2cd4b	C	T	9: 67,760,289	A189V	probably benign	Het
Camk2b	C	T	11: 5,972,321	R556H	probably damaging	Het
Cfap126	A	G	1: 171,126,164	D101G	possibly damaging	Het
Chd5	A	T	4: 152,374,434	I1085F	probably damaging	Het
Chp2	A	G	7: 122,221,869	E151G	probably damaging	Het
Chrnb2	C	T	3: 89,761,315	R231H	possibly damaging	Het
Crisp4	T	A	1: 18,137,035	I10F	possibly damaging	Het
Csnka2ip	T	A	16: 64,478,570	H477L	unknown	Het
Ctu1	T	A	7: 43,675,238	F34I	probably damaging	Het
Dctn1	T	A	6: 83,191,281	S407T	possibly damaging	Het
E330021D16Rik	T	C	6: 136,401,274	N186S	probably benign	Het
Ech1	T	C	7: 28,830,264	F191L	probably benign	Het
Enpp3	T	C	10: 24,808,166	D60G	probably damaging	Het
Epha6	T	C	16: 60,425,170	Y222C	possibly damaging	Het
Eppk1	A	T	15: 76,109,223	W1153R	probably benign	Het
Fbxo4	C	T	15: 3,977,955	D76N	probably damaging	Het
Fndc7	G	A	3: 108,876,648	A215V	probably benign	Het
Gemin5	C	T	11: 58,125,121	R1352Q	probably benign	Het
Gm4969	A	G	7: 19,102,375		probably benign	Het
Gm9639	T	C	10: 77,794,691		probably benign	Het
Gm973	C	A	1: 59,634,092	Q160K	unknown	Het
Gpatch2l	G	A	12: 86,244,184	R47H	probably damaging	Het
Grid2	A	T	6: 64,076,909	Q364L	possibly damaging	Het
Kcnn2	T	G	18: 45,592,377	S313R	probably damaging	Het
Kera	T	C	10: 97,608,952	Y58H	probably damaging	Het
Mtfr2	T	C	10: 20,354,116	L105P	probably benign	Het
Myom2	A	G	8: 15,084,531	T445A	probably benign	Het
Olfr1394	A	G	11: 49,160,412	R133G	possibly damaging	Het
Olfr905	T	A	9: 38,473,239	L164Q	probably damaging	Het
Pcdha12	T	C	18: 37,020,276	L16P	probably benign	Het
Pcdhb10	T	C	18: 37,413,118	Y416H	probably damaging	Het
Pde8b	T	C	13: 95,086,834	Y304C	possibly damaging	Het
Pkd1	T	C	17: 24,578,501	I2605T	possibly damaging	Het
Pnn	T	C	12: 59,070,299		probably null	Het
Ppa1	G	A	10: 61,661,017	G95S	probably damaging	Het
Rapgef4	G	T	2: 72,239,125	A730S	probably damaging	Het
Scap	A	G	9: 110,384,647	Y1226C	probably damaging	Het
Scn2a	A	T	2: 65,682,109	T197S	probably benign	Het
Slc2a6	GCTTCC	GC	2: 27,026,035		probably null	Het
Slc8a3	T	C	12: 81,314,755	Y430C	probably benign	Het
Tead3	T	C	17: 28,341,532	T33A	probably benign	Het
Tep1	T	A	14: 50,850,705	I792F	possibly damaging	Het
Trpm2	A	T	10: 77,935,891	I638N	probably damaging	Het
Tuba1c	A	G	15: 99,037,312	D218G	probably benign	Het
Tubgcp4	T	A	2: 121,192,297	W495R	probably damaging	Het
Tut1	T	C	19: 8,966,018	L823P	probably damaging	Het
Umodl1	C	T	17: 30,999,123	A1228V	probably damaging	Het
Vmn1r235	T	A	17: 21,261,865	F151I	probably benign	Het
Vmn2r45	T	A	7: 8,483,220	K356N	probably benign	Het
Zfp318	T	A	17: 46,400,043	N897K	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
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'- GTGACACAGAAGATTCCTTGC -3'
(R):5'- GGTGATGTATCCACTGATGCG -3'

Sequencing Primer
(F):5'- TTTGCTGCTCTTCCGGGGTC -3'
(R):5'- TCTCTAGGACCATCTGCAGC -3'

Posted On

2019-05-13