Incidental Mutation 'R0016:Chrd'
| ID |
32726 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Chrd
|
| Ensembl Gene |
ENSMUSG00000006958 |
| Gene Name |
chordin |
| Synonyms |
Chd |
| MMRRC Submission |
038311-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R0016 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
(trace)
|
| Chromosome |
16 |
| Chromosomal Location |
20551877-20561134 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to C
at 20553058 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Leucine
at position 162
(V162L)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000156323
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000007171]
[ENSMUST00000076422]
[ENSMUST00000115423]
[ENSMUST00000115437]
[ENSMUST00000153299]
[ENSMUST00000231636]
[ENSMUST00000232646]
[ENSMUST00000231698]
[ENSMUST00000231826]
[ENSMUST00000232217]
|
| AlphaFold |
Q9Z0E2 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000007171
AA Change: V140L
PolyPhen 2
Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000007171
Gene: ENSMUSG00000006958
AA Change: V140L
| 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: ENSMUST00000076422
|
| SMART Domains |
Protein: ENSMUSP00000075756
Gene: ENSMUSG00000022847
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
21 |
N/A |
INTRINSIC |
|
Pfam:EPO_TPO
|
24 |
188 |
9.4e-78 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000115423
AA Change: V140L
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000111083
Gene: ENSMUSG00000006958
AA Change: V140L
| 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
AA Change: V140L
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000138259
Gene: ENSMUSG00000006958
AA Change: V140L
| 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
AA Change: V140L
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000232646
AA Change: V162L
PolyPhen 2
Score 0.021 (Sensitivity: 0.95; Specificity: 0.80)
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000231698
AA Change: V162L
PolyPhen 2
Score 0.846 (Sensitivity: 0.83; Specificity: 0.93)
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232104
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000231826
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232020
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000232217
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000231689
|
| Meta Mutation Damage Score |
0.1795 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.3%
- 10x: 96.4%
- 20x: 93.2%
|
| Validation Efficiency |
100% (58/58) |
| 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: 58 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca12 |
A |
C |
1: 71,333,959 (GRCm39) |
V1181G |
probably benign |
Het |
| Adamts12 |
A |
T |
15: 11,217,915 (GRCm39) |
I291F |
probably damaging |
Het |
| Aspm |
G |
C |
1: 139,407,282 (GRCm39) |
Q2056H |
probably benign |
Het |
| C7 |
A |
T |
15: 5,076,406 (GRCm39) |
V122E |
probably benign |
Het |
| Casp12 |
A |
T |
9: 5,352,844 (GRCm39) |
Q152L |
probably null |
Het |
| Cdh16 |
T |
A |
8: 105,344,264 (GRCm39) |
T92S |
probably benign |
Het |
| Cpne8 |
A |
G |
15: 90,385,608 (GRCm39) |
|
probably benign |
Het |
| Cspg4b |
T |
C |
13: 113,502,639 (GRCm39) |
Y115H |
probably damaging |
Het |
| Cyp2j7 |
T |
A |
4: 96,090,384 (GRCm39) |
I347F |
probably damaging |
Het |
| Cyp4a10 |
A |
T |
4: 115,378,304 (GRCm39) |
Q130L |
probably damaging |
Het |
| Dach1 |
C |
T |
14: 98,406,184 (GRCm39) |
G188R |
probably damaging |
Het |
| Dgkd |
T |
C |
1: 87,845,674 (GRCm39) |
S294P |
probably benign |
Het |
| Dnah8 |
A |
G |
17: 30,882,290 (GRCm39) |
I621V |
probably benign |
Het |
| Dync2h1 |
A |
G |
9: 7,144,346 (GRCm39) |
|
probably benign |
Het |
| Echdc1 |
A |
T |
10: 29,198,417 (GRCm39) |
|
probably benign |
Het |
| Elovl3 |
T |
A |
19: 46,120,597 (GRCm39) |
F30Y |
probably damaging |
Het |
| Fa2h |
T |
C |
8: 112,120,146 (GRCm39) |
Y80C |
probably damaging |
Het |
| Fgd3 |
C |
T |
13: 49,450,085 (GRCm39) |
D55N |
probably benign |
Het |
| Fhod1 |
T |
C |
8: 106,058,287 (GRCm39) |
E823G |
possibly damaging |
Het |
| Gapvd1 |
A |
G |
2: 34,589,925 (GRCm39) |
|
probably benign |
Het |
| Gm17067 |
A |
T |
7: 42,358,046 (GRCm39) |
I152K |
probably benign |
Het |
| Gvin3 |
G |
A |
7: 106,202,453 (GRCm39) |
L264F |
probably benign |
Het |
| Kif27 |
A |
G |
13: 58,502,528 (GRCm39) |
V50A |
probably damaging |
Het |
| Kpna2 |
T |
C |
11: 106,881,912 (GRCm39) |
T305A |
probably benign |
Het |
| Krtap22-2 |
A |
G |
16: 88,807,407 (GRCm39) |
|
probably benign |
Het |
| Lrp2bp |
T |
A |
8: 46,465,068 (GRCm39) |
F62L |
probably damaging |
Het |
| Marf1 |
G |
A |
16: 13,970,129 (GRCm39) |
H197Y |
probably damaging |
Het |
| Mob3b |
A |
G |
4: 35,083,947 (GRCm39) |
F81L |
probably benign |
Het |
| Mon2 |
C |
T |
10: 122,871,451 (GRCm39) |
V389M |
probably damaging |
Het |
| Myef2l |
A |
T |
3: 10,154,379 (GRCm39) |
M383L |
possibly damaging |
Het |
| Myh8 |
A |
G |
11: 67,189,351 (GRCm39) |
K1176E |
probably damaging |
Het |
| Naf1 |
T |
C |
8: 67,341,707 (GRCm39) |
|
probably benign |
Het |
| Nckap1l |
A |
G |
15: 103,384,063 (GRCm39) |
T554A |
probably benign |
Het |
| Oog3 |
A |
G |
4: 143,884,641 (GRCm39) |
Y432H |
probably damaging |
Het |
| Paxbp1 |
A |
T |
16: 90,832,924 (GRCm39) |
|
probably benign |
Het |
| Phf20 |
A |
T |
2: 156,109,114 (GRCm39) |
K154* |
probably null |
Het |
| Pip4p1 |
C |
T |
14: 51,166,351 (GRCm39) |
R213Q |
probably damaging |
Het |
| Plekhj1 |
T |
C |
10: 80,632,250 (GRCm39) |
D74G |
possibly damaging |
Het |
| Plpp4 |
T |
C |
7: 128,925,148 (GRCm39) |
C128R |
probably damaging |
Het |
| Rcan3 |
A |
T |
4: 135,145,689 (GRCm39) |
|
probably null |
Het |
| Sh3rf1 |
T |
A |
8: 61,827,172 (GRCm39) |
M642K |
probably benign |
Het |
| Slc7a1 |
A |
G |
5: 148,271,393 (GRCm39) |
V522A |
probably benign |
Het |
| Sorbs1 |
A |
G |
19: 40,303,182 (GRCm39) |
|
probably benign |
Het |
| Spry2 |
C |
T |
14: 106,130,731 (GRCm39) |
V152M |
probably benign |
Het |
| Srgap2 |
A |
G |
1: 131,277,200 (GRCm39) |
M349T |
possibly damaging |
Het |
| Stag3 |
A |
G |
5: 138,289,643 (GRCm39) |
H271R |
possibly damaging |
Het |
| Stat4 |
T |
C |
1: 52,107,939 (GRCm39) |
V136A |
probably benign |
Het |
| Stc2 |
A |
T |
11: 31,310,177 (GRCm39) |
D286E |
probably benign |
Het |
| Stk31 |
T |
C |
6: 49,414,311 (GRCm39) |
Y482H |
probably damaging |
Het |
| Tasor2 |
A |
C |
13: 3,635,170 (GRCm39) |
|
probably null |
Het |
| Ticrr |
C |
T |
7: 79,343,540 (GRCm39) |
P1135L |
probably benign |
Het |
| Trim27 |
A |
T |
13: 21,375,399 (GRCm39) |
E310V |
probably benign |
Het |
| Uvrag |
T |
C |
7: 98,641,188 (GRCm39) |
K284R |
probably benign |
Het |
| Vmn1r78 |
A |
C |
7: 11,887,279 (GRCm39) |
S297R |
probably benign |
Het |
| Xylt2 |
A |
G |
11: 94,560,466 (GRCm39) |
S270P |
probably damaging |
Het |
| Zfhx3 |
T |
C |
8: 109,676,810 (GRCm39) |
M2620T |
probably benign |
Het |
| Zkscan2 |
C |
A |
7: 123,099,219 (GRCm39) |
|
probably benign |
Het |
| Zwint |
T |
C |
10: 72,493,030 (GRCm39) |
|
probably benign |
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 |
|
|
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 |
|
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'- GCTGCAAGAACATCAAACCTCAGTG -3'
(R):5'- GCGCCACAAAGTCTTCGAGAAGAG -3'
Sequencing Primer
(F):5'- AGGACACTGCTGCCAGAC -3'
(R):5'- GAAGATGGCCTGAGCACTG -3'
|
| Posted On |
2013-05-09 |
Incidental Mutation