Incidental Mutation 'R7813:Chrd'
ID 628607
Institutional Source Beutler Lab
Gene Symbol Chrd
Ensembl Gene ENSMUSG00000006958
Gene Name chordin
Synonyms Chd
MMRRC Submission 045868-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7813 (G1)
Quality Score 225.009
Status Validated
Chromosome 16
Chromosomal Location 20551877-20561134 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 20554155 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 336 (T336A)
Ref Sequence ENSEMBL: ENSMUSP00000156323 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000007171] [ENSMUST00000076422] [ENSMUST00000115423] [ENSMUST00000115437] [ENSMUST00000153299] [ENSMUST00000231636] [ENSMUST00000231698] [ENSMUST00000231826] [ENSMUST00000232217] [ENSMUST00000232646]
AlphaFold Q9Z0E2
Predicted Effect silent
Transcript: ENSMUST00000007171
SMART Domains Protein: ENSMUSP00000007171
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 528 643 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 silent
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 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 probably benign
Transcript: ENSMUST00000231698
AA Change: T336A

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
Predicted Effect probably benign
Transcript: ENSMUST00000231826
Predicted Effect probably benign
Transcript: ENSMUST00000232217
Predicted Effect silent
Transcript: ENSMUST00000232646
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.4%
Validation Efficiency 100% (60/60)
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
GeneRefVarChr/LocMutationPredicted EffectZygosity
9330159F19Rik G A 10: 29,100,896 (GRCm39) R423K probably benign Het
Acot7 T C 4: 152,307,575 (GRCm39) S170P probably damaging Het
Arhgap40 A G 2: 158,380,620 (GRCm39) Q341R probably benign Het
Arhgef28 T C 13: 98,082,189 (GRCm39) E1206G possibly damaging Het
Arpp21 T A 9: 112,008,133 (GRCm39) K122N probably damaging Het
Arsi T C 18: 61,049,726 (GRCm39) L203P possibly damaging Het
C1rb A T 6: 124,557,488 (GRCm39) I542F probably benign Het
Cadm3 C A 1: 173,171,956 (GRCm39) V206L probably benign Het
Card11 T C 5: 140,885,419 (GRCm39) D380G probably damaging Het
Ccdc42 A T 11: 68,488,534 (GRCm39) Q164L probably benign Het
Ccnd1 A G 7: 144,491,622 (GRCm39) probably null Het
Cep120 T C 18: 53,871,578 (GRCm39) D98G probably damaging Het
Clca3a2 C A 3: 144,790,726 (GRCm39) A449S probably benign Het
Dnah7a A G 1: 53,657,245 (GRCm39) F844L probably benign Het
Fbxo11 T A 17: 88,308,245 (GRCm39) I480F Het
Fcrl5 A G 3: 87,350,930 (GRCm39) T147A probably benign Het
Gm15130 T A 2: 110,969,320 (GRCm39) I133F Het
Gpr155 C T 2: 73,212,329 (GRCm39) W98* probably null Het
Hspa4 A G 11: 53,162,863 (GRCm39) S408P probably damaging Het
Il12rb2 G A 6: 67,333,635 (GRCm39) R215C possibly damaging Het
Itga5 T A 15: 103,265,741 (GRCm39) probably null Het
Kcnip3 T A 2: 127,323,703 (GRCm39) probably null Het
Krt12 A G 11: 99,309,309 (GRCm39) probably null Het
Marchf3 A T 18: 56,916,163 (GRCm39) S177R probably benign Het
Minpp1 T G 19: 32,468,803 (GRCm39) F229V probably damaging Het
Muc2 G A 7: 141,282,543 (GRCm39) probably null Het
Myh10 A G 11: 68,676,735 (GRCm39) T906A probably benign Het
Myh13 A G 11: 67,218,056 (GRCm39) D43G probably benign Het
Nacad C T 11: 6,549,071 (GRCm39) D1327N probably benign Het
Nbeal1 A T 1: 60,331,048 (GRCm39) Y2219F probably damaging Het
Nckap5 A G 1: 125,953,163 (GRCm39) S1130P probably benign Het
Pfkfb3 T C 2: 11,486,719 (GRCm39) N415S probably benign Het
Plxdc2 A G 2: 16,665,678 (GRCm39) I293V possibly damaging Het
Prpf38a A T 4: 108,436,277 (GRCm39) I12N probably damaging Het
Ptprt C T 2: 161,372,413 (GRCm39) V1420M probably damaging Het
Qars1 A G 9: 108,386,670 (GRCm39) D161G probably damaging Het
Scaf8 T A 17: 3,247,549 (GRCm39) D957E probably damaging Het
Scn7a T C 2: 66,506,689 (GRCm39) Y1400C probably damaging Het
Sis T C 3: 72,832,801 (GRCm39) I999V probably benign Het
Sorcs2 A T 5: 36,181,958 (GRCm39) L1054H probably damaging Het
Sptbn1 C T 11: 30,088,455 (GRCm39) A906T probably damaging Het
Srd5a2 A G 17: 74,331,541 (GRCm39) F152S probably benign Het
Stkld1 T A 2: 26,835,888 (GRCm39) L241* probably null Het
Strip2 A T 6: 29,923,912 (GRCm39) probably null Het
Tcaf1 A C 6: 42,650,363 (GRCm39) Y905* probably null Het
Tet2 T C 3: 133,179,404 (GRCm39) I1254V probably benign Het
Tiam2 A T 17: 3,487,522 (GRCm39) N681I probably damaging Het
Trappc6a A G 7: 19,248,124 (GRCm39) probably null Het
Trav12-2 A T 14: 53,854,223 (GRCm39) K66* probably null Het
Ttn T A 2: 76,597,841 (GRCm39) I19691F probably damaging Het
Tubgcp5 A T 7: 55,450,444 (GRCm39) Q185L possibly damaging Het
Vmn1r44 A T 6: 89,869,192 (GRCm39) probably benign Het
Vps13a T C 19: 16,628,820 (GRCm39) D2717G possibly damaging Het
Vps13d A T 4: 144,904,633 (GRCm39) Y133* probably null Het
Zer1 T C 2: 30,000,385 (GRCm39) D265G probably damaging Het
Zfp710 A G 7: 79,730,859 (GRCm39) D12G possibly damaging Het
Zfp819 T C 7: 43,266,191 (GRCm39) S225P 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
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
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
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'- GTAGCCCTTGTGACATCCAC -3'
(R):5'- AGCTAGTCCTGCAAGCACTG -3'

Sequencing Primer
(F):5'- GTGACATCCACTCACCCTTCAGG -3'
(R):5'- AGCACTGCACATGTGAGCATTTC -3'
Posted On 2020-05-18