Incidental Mutation 'R3406:Ncdn'
| ID |
259377 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ncdn
|
| Ensembl Gene |
ENSMUSG00000028833 |
| Gene Name |
neurochondrin |
| Synonyms |
neurochondrin-2, neurochondrin-1, norbin |
| MMRRC Submission |
040624-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R3406 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
126637543-126647231 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 126642388 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Glutamine
at position 423
(R423Q)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000101722
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030637]
[ENSMUST00000102608]
[ENSMUST00000106116]
[ENSMUST00000148935]
[ENSMUST00000154640]
|
| AlphaFold |
Q9Z0E0 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000030637
AA Change: R423Q
PolyPhen 2
Score 0.093 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000030637
Gene: ENSMUSG00000028833
AA Change: R423Q
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Neurochondrin
|
30 |
637 |
3e-209 |
PFAM |
|
low complexity region
|
649 |
659 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000102608
|
| SMART Domains |
Protein: ENSMUSP00000099668
Gene: ENSMUSG00000028830
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
83 |
97 |
N/A |
INTRINSIC |
|
FN3
|
113 |
391 |
8.45e1 |
SMART |
|
IG_like
|
305 |
398 |
3.57e1 |
SMART |
|
PKD
|
309 |
400 |
3.1e-1 |
SMART |
|
FN3
|
399 |
485 |
2.7e1 |
SMART |
|
PKD
|
408 |
497 |
1.87e-4 |
SMART |
|
FN3
|
502 |
676 |
4.47e1 |
SMART |
|
PKD
|
503 |
593 |
3.22e-8 |
SMART |
|
IG_like
|
508 |
591 |
1.17e1 |
SMART |
|
IG_like
|
597 |
782 |
1.66e2 |
SMART |
|
PKD
|
599 |
687 |
8.98e-7 |
SMART |
|
PKD
|
693 |
784 |
1.05e-7 |
SMART |
|
FN3
|
694 |
772 |
3.71e1 |
SMART |
|
transmembrane domain
|
927 |
949 |
N/A |
INTRINSIC |
|
low complexity region
|
995 |
1010 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000106116
AA Change: R423Q
PolyPhen 2
Score 0.093 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000101722
Gene: ENSMUSG00000028833
AA Change: R423Q
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Neurochondrin
|
30 |
637 |
9.1e-217 |
PFAM |
|
low complexity region
|
649 |
659 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000127079
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000148935
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000154640
|
| SMART Domains |
Protein: ENSMUSP00000122352
Gene: ENSMUSG00000028830
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
83 |
97 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.9%
- 20x: 93.4%
|
| Validation Efficiency |
98% (52/53) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a leucine-rich cytoplasmic protein, which is highly similar to a mouse protein that negatively regulates Ca/calmodulin-dependent protein kinase II phosphorylation and may be essential for spatial learning processes. Several alternatively spliced transcript variants of this gene have been described. [provided by RefSeq, Jul 2008]
PHENOTYPE: Targeted inactivation of this gene results in early embryonic lethality in the homozygous state and impaired chondrocyte proliferation and differentiation in the heterozygous state. Gene trap mutation resulted in lacrimal gland hypertrophy. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abhd18 |
T |
A |
3: 40,859,338 (GRCm39) |
M1K |
probably null |
Het |
| Adam34l |
A |
T |
8: 44,079,089 (GRCm39) |
C378* |
probably null |
Het |
| Bdkrb2 |
T |
C |
12: 105,558,755 (GRCm39) |
V332A |
possibly damaging |
Het |
| Cdc27 |
T |
C |
11: 104,398,026 (GRCm39) |
E778G |
probably damaging |
Het |
| Chd4 |
C |
A |
6: 125,098,970 (GRCm39) |
T1586K |
probably benign |
Het |
| Cnga3 |
A |
G |
1: 37,301,146 (GRCm39) |
E622G |
probably benign |
Het |
| Dbh |
A |
G |
2: 27,064,977 (GRCm39) |
D396G |
possibly damaging |
Het |
| Dhodh |
G |
A |
8: 110,330,107 (GRCm39) |
R86* |
probably null |
Het |
| Dpt |
A |
C |
1: 164,624,500 (GRCm39) |
E67A |
probably damaging |
Het |
| Eif2ak2 |
A |
G |
17: 79,166,068 (GRCm39) |
|
probably benign |
Het |
| Esp4 |
T |
A |
17: 40,913,336 (GRCm39) |
L68M |
possibly damaging |
Het |
| Exo1 |
A |
G |
1: 175,733,536 (GRCm39) |
K787E |
possibly damaging |
Het |
| Fbxo38 |
T |
C |
18: 62,647,914 (GRCm39) |
T875A |
probably damaging |
Het |
| Gsdma |
T |
C |
11: 98,563,964 (GRCm39) |
|
probably benign |
Het |
| Hemk1 |
G |
A |
9: 107,214,415 (GRCm39) |
Q6* |
probably null |
Het |
| Hmcn2 |
C |
T |
2: 31,323,284 (GRCm39) |
|
probably benign |
Het |
| Hook2 |
A |
G |
8: 85,720,613 (GRCm39) |
|
probably benign |
Het |
| Irx3 |
A |
G |
8: 92,525,555 (GRCm39) |
S507P |
unknown |
Het |
| Kazn |
C |
A |
4: 141,966,506 (GRCm39) |
|
probably benign |
Het |
| Kcne4 |
C |
T |
1: 78,795,688 (GRCm39) |
A112V |
possibly damaging |
Het |
| Lamb1 |
C |
T |
12: 31,337,528 (GRCm39) |
R372C |
probably damaging |
Het |
| Lrrc30 |
A |
G |
17: 67,939,175 (GRCm39) |
L135P |
probably damaging |
Het |
| Lyst |
T |
A |
13: 13,809,815 (GRCm39) |
M495K |
possibly damaging |
Het |
| Mab21l3 |
C |
A |
3: 101,730,847 (GRCm39) |
V131F |
probably damaging |
Het |
| Mki67 |
T |
A |
7: 135,309,204 (GRCm39) |
T416S |
probably benign |
Het |
| Mlst8 |
A |
T |
17: 24,697,099 (GRCm39) |
M56K |
probably benign |
Het |
| Mmp9 |
A |
G |
2: 164,791,310 (GRCm39) |
Y160C |
probably damaging |
Het |
| Mslnl |
A |
G |
17: 25,965,155 (GRCm39) |
Y507C |
probably damaging |
Het |
| Muc6 |
G |
A |
7: 141,218,313 (GRCm39) |
S2120F |
possibly damaging |
Het |
| Myl12a |
A |
T |
17: 71,301,737 (GRCm39) |
M130K |
probably benign |
Het |
| Nalf2 |
A |
G |
X: 98,889,109 (GRCm39) |
I325V |
probably benign |
Het |
| Ncf2 |
A |
G |
1: 152,701,698 (GRCm39) |
|
probably benign |
Het |
| Nek8 |
G |
T |
11: 78,061,572 (GRCm39) |
S319* |
probably null |
Het |
| Or11g7 |
G |
A |
14: 50,690,653 (GRCm39) |
C48Y |
probably benign |
Het |
| Or52m2 |
T |
C |
7: 102,263,993 (GRCm39) |
M68V |
possibly damaging |
Het |
| Pcdh17 |
T |
A |
14: 84,684,062 (GRCm39) |
D176E |
probably damaging |
Het |
| Pcdhb15 |
C |
A |
18: 37,608,442 (GRCm39) |
A558E |
probably benign |
Het |
| Plrg1 |
T |
A |
3: 82,978,526 (GRCm39) |
W431R |
probably damaging |
Het |
| Rbfox3 |
T |
A |
11: 118,387,283 (GRCm39) |
Q277L |
possibly damaging |
Het |
| Rpgrip1 |
G |
A |
14: 52,382,666 (GRCm39) |
D600N |
possibly damaging |
Het |
| Siah3 |
A |
G |
14: 75,763,421 (GRCm39) |
D224G |
probably damaging |
Het |
| Slc22a6 |
T |
C |
19: 8,598,675 (GRCm39) |
L244P |
probably damaging |
Het |
| Stap2 |
A |
T |
17: 56,304,511 (GRCm39) |
W374R |
probably benign |
Het |
| Tbck |
T |
A |
3: 132,432,845 (GRCm39) |
N418K |
probably benign |
Het |
| Tcp11x2 |
T |
C |
X: 134,555,733 (GRCm39) |
N474S |
probably damaging |
Het |
| Tenm3 |
A |
C |
8: 48,681,590 (GRCm39) |
V2680G |
probably damaging |
Het |
| Thada |
A |
T |
17: 84,538,213 (GRCm39) |
|
probably benign |
Het |
| Tlr6 |
C |
T |
5: 65,110,772 (GRCm39) |
V712M |
probably damaging |
Het |
| Uvssa |
G |
T |
5: 33,547,162 (GRCm39) |
G243C |
probably damaging |
Het |
| Vwa8 |
T |
A |
14: 79,401,660 (GRCm39) |
|
probably benign |
Het |
| Znrf2 |
A |
T |
6: 54,861,776 (GRCm39) |
N229I |
probably damaging |
Het |
|
| Other mutations in Ncdn |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00340:Ncdn
|
APN |
4 |
126,640,981 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0031:Ncdn
|
UTSW |
4 |
126,643,901 (GRCm39) |
splice site |
probably null |
|
|
R0135:Ncdn
|
UTSW |
4 |
126,640,462 (GRCm39) |
missense |
probably benign |
0.37 |
|
R0413:Ncdn
|
UTSW |
4 |
126,644,327 (GRCm39) |
missense |
possibly damaging |
0.52 |
|
R1404:Ncdn
|
UTSW |
4 |
126,643,833 (GRCm39) |
missense |
probably benign |
0.33 |
|
R1404:Ncdn
|
UTSW |
4 |
126,643,833 (GRCm39) |
missense |
probably benign |
0.33 |
|
R1486:Ncdn
|
UTSW |
4 |
126,642,391 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1533:Ncdn
|
UTSW |
4 |
126,642,491 (GRCm39) |
nonsense |
probably null |
|
|
R1785:Ncdn
|
UTSW |
4 |
126,639,066 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R1786:Ncdn
|
UTSW |
4 |
126,639,066 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R1789:Ncdn
|
UTSW |
4 |
126,645,796 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1791:Ncdn
|
UTSW |
4 |
126,645,732 (GRCm39) |
critical splice donor site |
probably null |
|
|
R4547:Ncdn
|
UTSW |
4 |
126,640,467 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4863:Ncdn
|
UTSW |
4 |
126,644,216 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4916:Ncdn
|
UTSW |
4 |
126,643,731 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R4917:Ncdn
|
UTSW |
4 |
126,643,731 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R4918:Ncdn
|
UTSW |
4 |
126,643,731 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R5218:Ncdn
|
UTSW |
4 |
126,644,603 (GRCm39) |
missense |
probably benign |
0.13 |
|
R5356:Ncdn
|
UTSW |
4 |
126,641,021 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5617:Ncdn
|
UTSW |
4 |
126,638,840 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R5718:Ncdn
|
UTSW |
4 |
126,643,743 (GRCm39) |
nonsense |
probably null |
|
|
R6057:Ncdn
|
UTSW |
4 |
126,638,824 (GRCm39) |
missense |
probably benign |
0.05 |
|
R6343:Ncdn
|
UTSW |
4 |
126,640,964 (GRCm39) |
missense |
possibly damaging |
0.74 |
|
R6986:Ncdn
|
UTSW |
4 |
126,641,022 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6988:Ncdn
|
UTSW |
4 |
126,640,982 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8257:Ncdn
|
UTSW |
4 |
126,643,676 (GRCm39) |
critical splice donor site |
probably null |
|
|
R8279:Ncdn
|
UTSW |
4 |
126,644,199 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8804:Ncdn
|
UTSW |
4 |
126,643,898 (GRCm39) |
missense |
probably benign |
0.09 |
|
R8812:Ncdn
|
UTSW |
4 |
126,638,905 (GRCm39) |
missense |
possibly damaging |
0.52 |
|
R9047:Ncdn
|
UTSW |
4 |
126,644,621 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
R9206:Ncdn
|
UTSW |
4 |
126,644,041 (GRCm39) |
missense |
probably benign |
0.03 |
|
R9208:Ncdn
|
UTSW |
4 |
126,644,041 (GRCm39) |
missense |
probably benign |
0.03 |
|
R9289:Ncdn
|
UTSW |
4 |
126,643,903 (GRCm39) |
missense |
possibly damaging |
0.81 |
|
R9353:Ncdn
|
UTSW |
4 |
126,644,464 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9420:Ncdn
|
UTSW |
4 |
126,645,762 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9578:Ncdn
|
UTSW |
4 |
126,645,795 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9687:Ncdn
|
UTSW |
4 |
126,642,467 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9698:Ncdn
|
UTSW |
4 |
126,643,688 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9778:Ncdn
|
UTSW |
4 |
126,642,467 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9781:Ncdn
|
UTSW |
4 |
126,642,467 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1176:Ncdn
|
UTSW |
4 |
126,643,946 (GRCm39) |
missense |
probably benign |
0.05 |
|
Z1176:Ncdn
|
UTSW |
4 |
126,643,944 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- ACATCAGGAGCCCAGGTTAG -3'
(R):5'- GTTCTGTTACTGGCAGGCAGAG -3'
Sequencing Primer
(F):5'- CTCCTAACTGCTGGGATTACAGG -3'
(R):5'- GCAGGCAGAGGAGGGTAC -3'
|
| Posted On |
2015-01-23 |
Incidental Mutation