Incidental Mutation 'R4707:Chrd'
ID 355377
Institutional Source Beutler Lab
Gene Symbol Chrd
Ensembl Gene ENSMUSG00000006958
Gene Name chordin
Synonyms Chd
MMRRC Submission 041955-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4707 (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 T at 20557558 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Phenylalanine at position 726 (I726F)
Ref Sequence ENSEMBL: ENSMUSP00000007171 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000007171] [ENSMUST00000115423] [ENSMUST00000115437] [ENSMUST00000153299] [ENSMUST00000231636] [ENSMUST00000232646] [ENSMUST00000231698]
AlphaFold Q9Z0E2
Predicted Effect possibly damaging
Transcript: ENSMUST00000007171
AA Change: I726F

PolyPhen 2 Score 0.577 (Sensitivity: 0.88; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000007171
Gene: ENSMUSG00000006958
AA Change: I726F

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: I748F

PolyPhen 2 Score 0.509 (Sensitivity: 0.88; Specificity: 0.90)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232020
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232104
Predicted Effect noncoding transcript
Transcript: ENSMUST00000231689
Predicted Effect probably benign
Transcript: ENSMUST00000231698
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.0%
  • 20x: 94.7%
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: 115 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700010I14Rik A G 17: 9,224,544 (GRCm39) K450R probably damaging Het
Abcd2 T C 15: 91,043,385 (GRCm39) D601G probably benign Het
Abcf3 A G 16: 20,367,808 (GRCm39) K56E possibly damaging Het
Acaca T C 11: 84,203,680 (GRCm39) V1477A probably damaging Het
Adamts20 G A 15: 94,231,528 (GRCm39) P887L possibly damaging Het
Ahnak T G 19: 8,994,099 (GRCm39) S5128A probably benign Het
Ahsa2 C A 11: 23,443,162 (GRCm39) V197F probably benign Het
Ak9 C A 10: 41,221,456 (GRCm39) H402N probably benign Het
Alpk1 G T 3: 127,481,241 (GRCm39) N175K possibly damaging Het
Als2 A G 1: 59,254,472 (GRCm39) V295A probably benign Het
Ankrd16 A G 2: 11,783,608 (GRCm39) D70G probably damaging Het
Apob A T 12: 8,056,205 (GRCm39) K1562N probably damaging Het
Arfgap2 C A 2: 91,100,316 (GRCm39) S250R probably damaging Het
Arhgef10l C T 4: 140,264,194 (GRCm39) M671I possibly damaging Het
Atrnl1 A G 19: 57,617,590 (GRCm39) I122V probably damaging Het
B4galnt2 C T 11: 95,766,923 (GRCm39) probably null Het
C8a A G 4: 104,713,618 (GRCm39) Y171H probably damaging Het
Cacnb4 A G 2: 52,364,927 (GRCm39) V112A probably benign Het
Capn9 G T 8: 125,340,195 (GRCm39) C566F possibly damaging Het
Ccdc88a T A 11: 29,397,956 (GRCm39) S230T probably benign Het
Cd300c2 A T 11: 114,887,811 (GRCm39) F197Y probably benign Het
Chd5 A G 4: 152,445,039 (GRCm39) Y340C probably damaging Het
Chrna10 G A 7: 101,762,426 (GRCm39) P255S possibly damaging Het
Clasp1 T A 1: 118,470,927 (GRCm39) Y197* probably null Het
Cyp2c69 C G 19: 39,837,852 (GRCm39) G410A probably benign Het
Cyp2e1 G A 7: 140,343,821 (GRCm39) V20I possibly damaging Het
Dapp1 T C 3: 137,638,928 (GRCm39) D225G probably benign Het
Dnah5 A T 15: 28,372,521 (GRCm39) D2924V probably damaging Het
Efcab12 A T 6: 115,791,510 (GRCm39) L554Q possibly damaging Het
Emsy T C 7: 98,246,311 (GRCm39) T228A possibly damaging Het
Evc2 G A 5: 37,579,204 (GRCm39) V1106I probably benign Het
Exoc8 G T 8: 125,624,209 (GRCm39) Q53K possibly damaging Het
Fbn2 A T 18: 58,189,344 (GRCm39) V1594D probably damaging Het
Fer1l4 T C 2: 155,887,543 (GRCm39) Y551C possibly damaging Het
Fhip1a G T 3: 85,595,877 (GRCm39) T115K probably damaging Het
Fmnl3 A G 15: 99,221,362 (GRCm39) M481T probably benign Het
Fras1 A G 5: 96,883,097 (GRCm39) N2543S probably damaging Het
Fsd2 T C 7: 81,209,428 (GRCm39) D138G probably damaging Het
Gda C T 19: 21,405,992 (GRCm39) V5I probably benign Het
Glt8d2 A T 10: 82,496,583 (GRCm39) D158E probably damaging Het
Gpx6 C T 13: 21,496,434 (GRCm39) Q3* probably null Het
Greb1l A G 18: 10,532,922 (GRCm39) M830V probably benign Het
Hnrnpul1 A C 7: 25,426,258 (GRCm39) V531G probably damaging Het
Ifi206 A T 1: 173,308,432 (GRCm39) H521Q probably benign Het
Igsf3 G C 3: 101,365,410 (GRCm39) R1127P probably benign Het
Il1rl1 A G 1: 40,489,348 (GRCm39) R367G probably damaging Het
Islr T C 9: 58,064,970 (GRCm39) D179G possibly damaging Het
Jcad G T 18: 4,649,338 (GRCm39) E70* probably null Het
Kcnd2 T C 6: 21,723,211 (GRCm39) I467T probably benign Het
Lrrc27 A G 7: 138,822,614 (GRCm39) T502A probably benign Het
Lrrtm3 T A 10: 63,923,781 (GRCm39) H462L probably benign Het
Mbd5 T C 2: 49,140,168 (GRCm39) L44S probably damaging Het
Mccc1 C A 3: 36,030,022 (GRCm39) M429I probably damaging Het
Mgam A T 6: 40,691,566 (GRCm39) probably null Het
Mipep T A 14: 61,109,552 (GRCm39) I643N probably damaging Het
Mmrn1 A T 6: 60,965,457 (GRCm39) I1162L probably benign Het
Mrc2 G A 11: 105,239,257 (GRCm39) probably null Het
Mug1 G A 6: 121,861,600 (GRCm39) C1354Y probably damaging Het
Nbeal2 A T 9: 110,461,123 (GRCm39) S1647T probably benign Het
Ndufaf2 C G 13: 108,189,314 (GRCm39) A145P probably damaging Het
Nedd9 A T 13: 41,492,051 (GRCm39) probably null Het
Nr4a2 T A 2: 57,002,105 (GRCm39) H116L probably benign Het
Nwd2 A G 5: 63,951,665 (GRCm39) Y232C probably damaging Het
Odf4 A G 11: 68,817,514 (GRCm39) L58P probably damaging Het
Or2a20 T A 6: 43,193,883 (GRCm39) V12D probably benign Het
Or4a27 T A 2: 88,559,056 (GRCm39) M296L possibly damaging Het
Or4c116 A T 2: 88,942,576 (GRCm39) F93L probably damaging Het
Or4g17 T A 2: 111,209,990 (GRCm39) L215H probably damaging Het
Or7e165 C T 9: 19,694,596 (GRCm39) H18Y probably damaging Het
Or8g24 A G 9: 38,989,558 (GRCm39) V161A probably benign Het
Or8s5 G T 15: 98,238,659 (GRCm39) H70Q possibly damaging Het
Orc6 T A 8: 86,029,579 (GRCm39) I41K probably damaging Het
Pikfyve A G 1: 65,307,005 (GRCm39) T1798A probably benign Het
Prdx6b T C 2: 80,123,404 (GRCm39) L71P probably damaging Het
Prmt2 A G 10: 76,062,055 (GRCm39) I50T probably damaging Het
Ptdss1 T C 13: 67,143,482 (GRCm39) probably null Het
Pygl T C 12: 70,254,532 (GRCm39) T138A possibly damaging Het
Rab3c T C 13: 110,198,434 (GRCm39) E198G probably benign Het
Rbl2 A G 8: 91,812,196 (GRCm39) Y255C probably damaging Het
Rev3l T A 10: 39,699,393 (GRCm39) S1297T probably damaging Het
Rgma C A 7: 73,067,564 (GRCm39) T367K probably damaging Het
Rps6ka5 C T 12: 100,564,144 (GRCm39) probably null Het
Rslcan18 A T 13: 67,246,590 (GRCm39) C217S probably damaging Het
Rtp3 A G 9: 110,815,279 (GRCm39) probably benign Het
Ryr1 A T 7: 28,745,087 (GRCm39) N3848K probably damaging Het
Sema6a T A 18: 47,381,779 (GRCm39) T923S probably benign Het
Serpinb6d A T 13: 33,855,336 (GRCm39) T337S possibly damaging Het
Sf3b1 G A 1: 55,029,666 (GRCm39) T1112M probably damaging Het
Shroom3 G T 5: 93,090,945 (GRCm39) V1151F probably damaging Het
Sidt1 A T 16: 44,090,221 (GRCm39) Y369* probably null Het
Slc16a6 A G 11: 109,354,193 (GRCm39) S59P probably benign Het
Slc25a17 A C 15: 81,211,527 (GRCm39) L163W probably damaging Het
Slc44a3 T C 3: 121,320,723 (GRCm39) T93A possibly damaging Het
Sptbn1 T C 11: 30,087,197 (GRCm39) T1081A possibly damaging Het
Sptbn4 T C 7: 27,116,431 (GRCm39) D456G probably benign Het
Sycp1 C A 3: 102,760,805 (GRCm39) A703S possibly damaging Het
Tas2r118 T A 6: 23,969,225 (GRCm39) M279L probably benign Het
Tc2n T G 12: 101,660,832 (GRCm39) Q133H probably benign Het
Tctn1 A G 5: 122,399,468 (GRCm39) probably null Het
Tenm4 A C 7: 96,423,253 (GRCm39) K683Q probably damaging Het
Tex10 A T 4: 48,468,984 (GRCm39) S64T probably benign Het
Tex15 A G 8: 34,072,525 (GRCm39) T2691A probably benign Het
Tmem175 A T 5: 108,790,016 (GRCm39) T123S probably damaging Het
Tsc1 C A 2: 28,562,419 (GRCm39) S348R probably damaging Het
Ttll4 A T 1: 74,718,166 (GRCm39) T6S possibly damaging Het
Ttll8 A T 15: 88,801,293 (GRCm39) I465N probably damaging Het
Ubr3 A G 2: 69,768,714 (GRCm39) probably benign Het
Ugdh A T 5: 65,580,695 (GRCm39) probably null Het
Usp34 T C 11: 23,437,215 (GRCm39) L3326S probably damaging Het
Vmn2r125 A T 4: 156,702,276 (GRCm39) I21F probably damaging Het
Vps9d1 G A 8: 123,975,351 (GRCm39) probably benign Het
Xab2 G A 8: 3,668,117 (GRCm39) R154C possibly damaging Het
Zbtb12 T C 17: 35,114,475 (GRCm39) S87P probably damaging Het
Zc3h12a A G 4: 125,014,686 (GRCm39) M266T probably damaging Het
Zfp108 G A 7: 23,959,837 (GRCm39) A143T probably benign 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
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
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'- TCAGAAGGAGTGCAGATGCC -3'
(R):5'- GACATTCACCTGGACACACG -3'

Sequencing Primer
(F):5'- AGGAGTGCAGATGCCCTTGG -3'
(R):5'- GACACACGGGACAGCACTG -3'
Posted On 2015-10-21