Incidental Mutation 'R6798:Chrd'
ID 533142
Institutional Source Beutler Lab
Gene Symbol Chrd
Ensembl Gene ENSMUSG00000006958
Gene Name chordin
Synonyms Chd
MMRRC Submission 044911-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6798 (G1)
Quality Score 222.009
Status Validated
Chromosome 16
Chromosomal Location 20551877-20561134 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 20553056 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Proline at position 139 (L139P)
Ref Sequence ENSEMBL: ENSMUSP00000138259 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000007171] [ENSMUST00000076422] [ENSMUST00000115423] [ENSMUST00000115437] [ENSMUST00000153299] [ENSMUST00000231636] [ENSMUST00000231698] [ENSMUST00000231826] [ENSMUST00000232217] [ENSMUST00000232646]
AlphaFold Q9Z0E2
Predicted Effect probably benign
Transcript: ENSMUST00000007171
AA Change: L139P

PolyPhen 2 Score 0.169 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000007171
Gene: ENSMUSG00000006958
AA Change: L139P

DomainStartEndE-ValueType
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: ENSMUST00000076422
SMART Domains Protein: ENSMUSP00000075756
Gene: ENSMUSG00000022847

DomainStartEndE-ValueType
signal peptide 1 21 N/A INTRINSIC
Pfam:EPO_TPO 24 188 9.4e-78 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000115423
AA Change: L139P

PolyPhen 2 Score 0.140 (Sensitivity: 0.92; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000111083
Gene: ENSMUSG00000006958
AA Change: L139P

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
signal peptide 1 21 N/A INTRINSIC
Pfam:EPO_TPO 25 193 5.4e-49 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000153299
AA Change: L139P

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000138259
Gene: ENSMUSG00000006958
AA Change: L139P

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
VWC 51 125 9.33e-2 SMART
Blast:CHRD 170 236 1e-21 BLAST
Predicted Effect noncoding transcript
Transcript: ENSMUST00000231636
AA Change: L139P
Predicted Effect noncoding transcript
Transcript: ENSMUST00000231698
AA Change: L161P
Predicted Effect noncoding transcript
Transcript: ENSMUST00000231826
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232217
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232646
AA Change: L161P
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.3%
  • 20x: 95.4%
Validation Efficiency 97% (73/75)
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: 74 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb1a T C 5: 8,782,364 (GRCm39) Y916H probably damaging Het
Adam11 A G 11: 102,667,834 (GRCm39) I740V probably damaging Het
Adam22 A T 5: 8,210,784 (GRCm39) D161E probably damaging Het
Agap3 A G 5: 24,703,280 (GRCm39) probably null Het
Ank2 T C 3: 126,737,913 (GRCm39) probably benign Het
Aspm T A 1: 139,396,423 (GRCm39) H867Q possibly damaging Het
Aurkaip1 T C 4: 155,917,196 (GRCm39) probably null Het
BC048507 A C 13: 68,011,683 (GRCm39) D20A probably benign Het
Cacna1a G A 8: 85,338,231 (GRCm39) A1704T probably damaging Het
Cep152 A C 2: 125,408,447 (GRCm39) probably null Het
Cep19 T C 16: 31,922,867 (GRCm39) probably null Het
Cfhr4 T C 1: 139,625,859 (GRCm39) T813A probably benign Het
Chd9 A T 8: 91,778,182 (GRCm39) E2731V possibly damaging Het
Cit A G 5: 116,064,585 (GRCm39) E489G possibly damaging Het
Clcn7 A G 17: 25,378,734 (GRCm39) N720D probably damaging Het
Col6a3 T C 1: 90,722,731 (GRCm39) probably null Het
Dchs2 T A 3: 83,255,593 (GRCm39) Y2430N probably damaging Het
Dpy30 A G 17: 74,614,751 (GRCm39) I64T probably damaging Het
Eif2b3 G T 4: 116,923,655 (GRCm39) W290L probably benign Het
Epha6 T G 16: 60,425,427 (GRCm39) E62A possibly damaging Het
Epha6 C T 16: 60,425,428 (GRCm39) E62K possibly damaging Het
Epha8 C T 4: 136,672,980 (GRCm39) R268Q probably benign Het
Fbxw17 C A 13: 50,587,300 (GRCm39) probably null Het
Fndc8 C T 11: 82,783,217 (GRCm39) T66I probably benign Het
Frmpd1 A G 4: 45,284,850 (GRCm39) T1224A probably benign Het
Gcm2 T C 13: 41,259,361 (GRCm39) D36G probably damaging Het
Glt28d2 T C 3: 85,779,296 (GRCm39) D59G probably benign Het
Gorasp1 T C 9: 119,758,663 (GRCm39) D243G probably benign Het
Gtsf1l T C 2: 162,929,391 (GRCm39) K31E probably benign Het
Heatr5a A G 12: 51,928,048 (GRCm39) V1816A probably benign Het
Il10ra T C 9: 45,167,730 (GRCm39) K274E probably damaging Het
Il1rl2 T C 1: 40,404,400 (GRCm39) I507T probably damaging Het
Jak3 T G 8: 72,133,615 (GRCm39) F408V probably damaging Het
Kdm1b A G 13: 47,222,012 (GRCm39) T484A probably benign Het
Lama5 G A 2: 179,833,455 (GRCm39) P1519L probably damaging Het
Map9 T G 3: 82,287,471 (GRCm39) L31W probably damaging Het
Mical2 T C 7: 111,975,266 (GRCm39) probably benign Het
Mt1 A G 8: 94,906,516 (GRCm39) probably benign Het
Myo18b T C 5: 112,909,252 (GRCm39) I1964V probably damaging Het
Nalf1 G A 8: 9,820,205 (GRCm39) Q272* probably null Het
Nod1 A T 6: 54,921,596 (GRCm39) C241S probably damaging Het
Nrxn1 T A 17: 90,937,378 (GRCm39) D685V probably damaging Het
Oog1 A T 12: 87,655,609 (GRCm39) probably null Het
Or11a4 T G 17: 37,536,697 (GRCm39) L227R probably damaging Het
Or2ag13 T C 7: 106,313,402 (GRCm39) Y162C probably damaging Het
Or4k2 A G 14: 50,424,584 (GRCm39) V30A probably benign Het
Or56b1b T A 7: 108,164,967 (GRCm39) K12* probably null Het
P4htm T A 9: 108,460,117 (GRCm39) N219I possibly damaging Het
Pcif1 T C 2: 164,727,711 (GRCm39) L168P possibly damaging Het
Pde4dip A G 3: 97,795,850 (GRCm39) V46A probably benign Het
Pias1 T C 9: 62,799,451 (GRCm39) T480A probably benign Het
Prkd2 A T 7: 16,583,128 (GRCm39) K297* probably null Het
Prl7d1 T A 13: 27,893,380 (GRCm39) probably null Het
Pxdc1 G T 13: 34,836,408 (GRCm39) A4E possibly damaging Het
Rcor1 A G 12: 111,006,320 (GRCm39) probably benign Het
Rev3l A T 10: 39,730,759 (GRCm39) D2761V probably damaging Het
Scgb1b7 A G 7: 31,412,406 (GRCm39) T61A probably damaging Het
Sec14l2 A G 11: 4,061,213 (GRCm39) Y83H probably damaging Het
Setd4 C A 16: 93,386,841 (GRCm39) V286F probably damaging Het
Slc22a29 A G 19: 8,137,968 (GRCm39) S536P probably benign Het
Snx25 T C 8: 46,486,810 (GRCm39) H977R probably damaging Het
Spint5 T A 2: 164,559,060 (GRCm39) C95* probably null Het
Sprr5 G C 3: 92,440,243 (GRCm39) C65W unknown Het
Srgap1 T C 10: 121,761,809 (GRCm39) D113G probably damaging Het
Stxbp2 T A 8: 3,691,180 (GRCm39) S476T probably benign Het
Tg A G 15: 66,550,688 (GRCm39) T273A probably damaging Het
Tnc C T 4: 63,883,841 (GRCm39) R1868H probably benign Het
Trappc10 A G 10: 78,024,665 (GRCm39) Y1155H probably benign Het
Trpm2 T A 10: 77,750,574 (GRCm39) N1341Y probably damaging Het
Vmn2r111 T C 17: 22,778,032 (GRCm39) N549S possibly damaging Het
Zfand1 T G 3: 10,411,236 (GRCm39) K67T probably benign Het
Zfand4 A C 6: 116,305,214 (GRCm39) K214Q probably benign Het
Zfp653 A T 9: 21,968,668 (GRCm39) V465E probably damaging Het
Zswim8 A G 14: 20,766,060 (GRCm39) Y782C probably damaging Het
Other mutations in Chrd
AlleleSourceChrCoordTypePredicted EffectPPH 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
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'- CAGGGTCAGCTGCAAGAACATC -3'
(R):5'- AAGATGGCCTGAGCACTGTC -3'

Sequencing Primer
(F):5'- ACACTGCTGCCAGACCTG -3'
(R):5'- TGAGCACTGTCAAGCCTTG -3'
Posted On 2018-08-29