Incidental Mutation 'R5204:Chrd'
| ID |
398378 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Chrd
|
| Ensembl Gene |
ENSMUSG00000006958 |
| Gene Name |
chordin |
| Synonyms |
Chd |
| MMRRC Submission |
042779-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5204 (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 20554822 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Phenylalanine
at position 413
(I413F)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000111083
(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: I413F
PolyPhen 2
Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)
|
| SMART Domains |
Protein: ENSMUSP00000007171
Gene: ENSMUSG00000006958
AA Change: I413F
| 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: I413F
PolyPhen 2
Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000111083
Gene: ENSMUSG00000006958
AA Change: I413F
| 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 |
noncoding transcript
Transcript: ENSMUST00000151150
|
| 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 |
noncoding transcript
Transcript: ENSMUST00000231689
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000232646
AA Change: I435F
PolyPhen 2
Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232020
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232104
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000231698
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.1%
- 20x: 95.0%
|
| 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: 36 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aarsd1 |
A |
T |
11: 101,297,752 (GRCm39) |
L532Q |
probably damaging |
Het |
| Abt1 |
G |
A |
13: 23,606,838 (GRCm39) |
R88C |
probably damaging |
Het |
| Aopep |
G |
A |
13: 63,180,904 (GRCm39) |
V289I |
probably benign |
Het |
| Arhgef7 |
T |
A |
8: 11,850,775 (GRCm39) |
L129* |
probably null |
Het |
| Arid1b |
T |
C |
17: 5,393,316 (GRCm39) |
V2282A |
probably damaging |
Het |
| Bivm |
G |
C |
1: 44,177,738 (GRCm39) |
G346A |
probably damaging |
Het |
| Cav1 |
T |
C |
6: 17,339,254 (GRCm39) |
L102P |
probably damaging |
Het |
| Ccdc57 |
A |
G |
11: 120,776,888 (GRCm39) |
V504A |
possibly damaging |
Het |
| Cd7 |
A |
T |
11: 120,928,860 (GRCm39) |
|
probably null |
Het |
| Cdh3 |
T |
C |
8: 107,270,871 (GRCm39) |
V508A |
probably benign |
Het |
| Clec4b1 |
T |
A |
6: 123,048,494 (GRCm39) |
*210R |
probably null |
Het |
| Clock |
A |
T |
5: 76,391,017 (GRCm39) |
|
probably null |
Het |
| Col4a2 |
T |
A |
8: 11,448,651 (GRCm39) |
|
probably null |
Het |
| Gpx7 |
T |
C |
4: 108,260,512 (GRCm39) |
T95A |
probably benign |
Het |
| Hivep3 |
T |
A |
4: 119,961,053 (GRCm39) |
|
probably null |
Het |
| Hrc |
A |
G |
7: 44,985,128 (GRCm39) |
Y93C |
possibly damaging |
Het |
| Igkv4-80 |
A |
C |
6: 68,993,649 (GRCm39) |
S81A |
probably benign |
Het |
| Klhl5 |
G |
T |
5: 65,288,781 (GRCm39) |
L14F |
possibly damaging |
Het |
| Mcm6 |
A |
G |
1: 128,261,375 (GRCm39) |
L743P |
probably benign |
Het |
| Nrxn1 |
A |
T |
17: 90,469,792 (GRCm39) |
F57Y |
probably damaging |
Het |
| Or51af1 |
C |
T |
7: 103,141,747 (GRCm39) |
V113M |
probably damaging |
Het |
| Otx1 |
C |
A |
11: 21,947,037 (GRCm39) |
A91S |
probably damaging |
Het |
| Pcdh20 |
G |
T |
14: 88,706,351 (GRCm39) |
D316E |
probably damaging |
Het |
| Pcdhb12 |
T |
A |
18: 37,569,142 (GRCm39) |
V96E |
probably damaging |
Het |
| Pi4ka |
A |
T |
16: 17,176,909 (GRCm39) |
L346M |
possibly damaging |
Het |
| Pkhd1l1 |
A |
C |
15: 44,410,437 (GRCm39) |
N2648T |
possibly damaging |
Het |
| Rufy1 |
C |
T |
11: 50,297,261 (GRCm39) |
R397Q |
probably damaging |
Het |
| Sema5a |
G |
T |
15: 32,686,793 (GRCm39) |
M968I |
probably benign |
Het |
| Slc33a1 |
A |
G |
3: 63,871,167 (GRCm39) |
Y149H |
probably damaging |
Het |
| Tln2 |
T |
A |
9: 67,261,764 (GRCm39) |
R658S |
probably benign |
Het |
| Tmem30c |
T |
C |
16: 57,090,385 (GRCm39) |
N274S |
possibly damaging |
Het |
| Tor3a |
A |
G |
1: 156,483,270 (GRCm39) |
L384P |
probably damaging |
Het |
| Trpm3 |
T |
A |
19: 22,425,705 (GRCm39) |
L20* |
probably null |
Het |
| Ttn |
T |
A |
2: 76,560,556 (GRCm39) |
I20955F |
probably damaging |
Het |
| Usp15 |
A |
T |
10: 122,949,545 (GRCm39) |
S908R |
probably benign |
Het |
| Zfp866 |
A |
G |
8: 70,218,690 (GRCm39) |
L310P |
probably damaging |
Het |
|
| Other mutations in Chrd |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH 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 |
|
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'- AGCTACGCATCAGTGGATAC -3'
(R):5'- TACCTACCACTTGCACCTGG -3'
Sequencing Primer
(F):5'- CACCAGGCAGAGCTGTGATG -3'
(R):5'- ACTTGCACCTGGTGGGCAG -3'
|
| Posted On |
2016-07-06 |
Incidental Mutation