Incidental Mutation 'R5445:Chrd'
ID 427428
Institutional Source Beutler Lab
Gene Symbol Chrd
Ensembl Gene ENSMUSG00000006958
Gene Name chordin
Synonyms Chd
MMRRC Submission 043010-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5445 (G1)
Quality Score 225
Status Not validated
Chromosome 16
Chromosomal Location 20551877-20561134 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 20557660 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 753 (T753A)
Ref Sequence ENSEMBL: ENSMUSP00000156080 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000007171] [ENSMUST00000115423] [ENSMUST00000115437] [ENSMUST00000153299] [ENSMUST00000231636] [ENSMUST00000232646] [ENSMUST00000231698]
AlphaFold Q9Z0E2
Predicted Effect probably benign
Transcript: ENSMUST00000007171
AA Change: T731A

PolyPhen 2 Score 0.415 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000007171
Gene: ENSMUSG00000006958
AA Change: T731A

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: ENSMUST00000115423
SMART Domains Protein: ENSMUSP00000111083
Gene: ENSMUSG00000006958

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 noncoding transcript
Transcript: ENSMUST00000151150
Predicted Effect probably benign
Transcript: ENSMUST00000153299
SMART Domains Protein: ENSMUSP00000138259
Gene: ENSMUSG00000006958

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 probably benign
Transcript: ENSMUST00000231636
Predicted Effect possibly damaging
Transcript: ENSMUST00000232646
AA Change: T753A

PolyPhen 2 Score 0.737 (Sensitivity: 0.85; Specificity: 0.92)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232104
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232020
Predicted Effect probably benign
Transcript: ENSMUST00000231698
Predicted Effect noncoding transcript
Transcript: ENSMUST00000231689
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 94.3%
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: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcg5 A T 17: 84,978,557 (GRCm39) D300E probably damaging Het
Apbb1ip T C 2: 22,725,960 (GRCm39) V244A possibly damaging Het
Arhgap32 T C 9: 32,159,678 (GRCm39) S232P probably benign Het
Atf7ip G A 6: 136,564,255 (GRCm39) V833M probably damaging Het
Casp7 A G 19: 56,421,770 (GRCm39) probably null Het
Ccdc9b T C 2: 118,590,067 (GRCm39) D259G probably damaging Het
Celsr2 T A 3: 108,299,974 (GRCm39) E2911D probably benign Het
Cep350 T C 1: 155,770,469 (GRCm39) D1807G probably benign Het
Cfap251 C T 5: 123,425,240 (GRCm39) T294M probably damaging Het
Clasp2 A G 9: 113,733,014 (GRCm39) D971G probably damaging Het
Cnnm2 A G 19: 46,865,727 (GRCm39) T772A possibly damaging Het
Cntn1 A T 15: 92,192,958 (GRCm39) N687Y probably damaging Het
Col6a3 G A 1: 90,709,761 (GRCm39) R1812* probably null Het
Dsc2 T C 18: 20,168,360 (GRCm39) I700V possibly damaging Het
Flt3 G A 5: 147,291,905 (GRCm39) Q540* probably null Het
Fmo4 T A 1: 162,632,842 (GRCm39) I170F probably benign Het
Fra10ac1 T A 19: 38,207,910 (GRCm39) D72V possibly damaging Het
Garin2 G A 12: 78,761,890 (GRCm39) E185K probably damaging Het
Gemin6 T G 17: 80,535,178 (GRCm39) V46G probably damaging Het
Gm2381 T G 7: 42,469,425 (GRCm39) H233P probably damaging Het
Gm5148 T A 3: 37,768,995 (GRCm39) Q75L probably damaging Het
Gm8369 T C 19: 11,482,170 (GRCm39) V27A possibly damaging Het
Gpr157 T C 4: 150,186,825 (GRCm39) S318P probably benign Het
Hectd4 G A 5: 121,404,337 (GRCm39) V405M probably benign Het
Hemgn T C 4: 46,400,738 (GRCm39) R41G probably benign Het
Hhipl1 T A 12: 108,294,467 (GRCm39) L791Q probably damaging Het
Hjurp T G 1: 88,194,038 (GRCm39) K290T probably benign Het
Ifi207 T C 1: 173,555,363 (GRCm39) E773G probably damaging Het
Kcnh6 T C 11: 105,914,685 (GRCm39) Y697H probably damaging Het
Lonrf2 T C 1: 38,846,234 (GRCm39) T313A probably benign Het
Lrba G T 3: 86,275,902 (GRCm39) V1757L probably benign Het
Lrrc24 T C 15: 76,600,306 (GRCm39) T278A probably benign Het
Ltbp2 T C 12: 84,856,428 (GRCm39) I679V probably null Het
Mapk4 G T 18: 74,064,073 (GRCm39) T383K probably benign Het
Mdn1 C T 4: 32,723,690 (GRCm39) P2542L probably damaging Het
Mia3 A G 1: 183,117,471 (GRCm39) V208A probably benign Het
Myo15a C A 11: 60,411,603 (GRCm39) C3234* probably null Het
Nlrp1b G T 11: 71,108,701 (GRCm39) Q267K probably benign Het
Nphp3 A G 9: 103,881,922 (GRCm39) K37E probably damaging Het
Nwd2 T C 5: 63,962,681 (GRCm39) M755T probably damaging Het
Or10u4 T A 10: 129,802,158 (GRCm39) H137L probably benign Het
Or52ac1 A G 7: 104,246,028 (GRCm39) F120S probably damaging Het
Or5p58 A G 7: 107,693,949 (GRCm39) V276A possibly damaging Het
Pdlim5 C T 3: 142,058,495 (GRCm39) R83K probably null Het
Plekha5 A T 6: 140,498,459 (GRCm39) R173* probably null Het
Pramel25 T A 4: 143,521,707 (GRCm39) V441E possibly damaging Het
Rbms3 T A 9: 117,080,853 (GRCm39) D6V possibly damaging Het
Rhoq A T 17: 87,271,755 (GRCm39) Y57F probably benign Het
Rrm1 A T 7: 102,100,230 (GRCm39) T204S possibly damaging Het
Slf1 A T 13: 77,239,323 (GRCm39) I447N probably benign Het
Smarcc2 T A 10: 128,323,943 (GRCm39) probably benign Het
Spdye4c C T 2: 128,438,484 (GRCm39) Q281* probably null Het
Tert T A 13: 73,792,403 (GRCm39) M890K probably benign Het
Tln1 C A 4: 43,543,905 (GRCm39) R1198L probably benign Het
Tmco4 A G 4: 138,748,178 (GRCm39) M253V probably damaging Het
Usp19 G T 9: 108,375,119 (GRCm39) V782F possibly damaging Het
Usp33 T A 3: 152,080,260 (GRCm39) S464T probably damaging Het
Usp47 A T 7: 111,673,928 (GRCm39) Y397F probably damaging Het
Vmn1r12 A G 6: 57,136,466 (GRCm39) T144A probably benign Het
Vmn2r90 A T 17: 17,954,386 (GRCm39) H850L probably benign Het
Zfhx3 A T 8: 109,682,842 (GRCm39) Q3427L unknown Het
Zfp236 G T 18: 82,700,281 (GRCm39) Q63K probably benign Het
Zfp7 T A 15: 76,775,054 (GRCm39) C365* probably null Het
Zfp786 T C 6: 47,796,619 (GRCm39) E773G 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
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
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'- ACATGTTTCTTCGAGGGGCAG -3'
(R):5'- TGGCTCCAGATTTGGTAGGC -3'

Sequencing Primer
(F):5'- TTCGAGGGGCAGCAGCG -3'
(R):5'- CGTTGTTTCTCTGTGGAGACAAAG -3'
Posted On 2016-09-01