Incidental Mutation 'R2903:Ift56'
| ID |
261550 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ift56
|
| Ensembl Gene |
ENSMUSG00000056832 |
| Gene Name |
intraflagellar transport 56 |
| Synonyms |
hpy, hydrocephalic-polydactyl, 9430097H08Rik, hop, Ttc26 |
| MMRRC Submission |
040490-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.583)
|
| Stock # |
R2903 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
6 |
| Chromosomal Location |
38358404-38404582 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 38378037 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 283
(V283A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000124369
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000159145]
[ENSMUST00000160215]
[ENSMUST00000162554]
|
| AlphaFold |
Q8BS45 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000159145
|
| SMART Domains |
Protein: ENSMUSP00000124873
Gene: ENSMUSG00000056832
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
19 |
29 |
N/A |
INTRINSIC |
|
Pfam:TPR_2
|
58 |
88 |
1.2e-5 |
PFAM |
|
Pfam:TPR_8
|
58 |
91 |
1.7e-3 |
PFAM |
|
Pfam:TPR_1
|
61 |
87 |
4.6e-4 |
PFAM |
|
Pfam:TPR_11
|
63 |
113 |
4.9e-11 |
PFAM |
|
Pfam:TPR_19
|
67 |
113 |
3.1e-7 |
PFAM |
|
Pfam:TPR_8
|
89 |
113 |
2e-3 |
PFAM |
|
Pfam:TPR_1
|
91 |
113 |
1.7e-4 |
PFAM |
|
Pfam:TPR_2
|
91 |
113 |
2.4e-3 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000160215
|
| SMART Domains |
Protein: ENSMUSP00000125097
Gene: ENSMUSG00000056832
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
19 |
29 |
N/A |
INTRINSIC |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000162554
AA Change: V283A
PolyPhen 2
Score 0.613 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000124369
Gene: ENSMUSG00000056832
AA Change: V283A
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
19 |
29 |
N/A |
INTRINSIC |
|
Pfam:TPR_2
|
58 |
88 |
2.7e-5 |
PFAM |
|
Pfam:TPR_11
|
63 |
117 |
9e-9 |
PFAM |
|
Pfam:TPR_9
|
157 |
227 |
9.2e-4 |
PFAM |
|
Blast:TPR
|
359 |
392 |
9e-10 |
BLAST |
|
Blast:TPR
|
461 |
494 |
8e-15 |
BLAST |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000162673
|
| Meta Mutation Damage Score |
0.0972 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.4%
- 20x: 95.4%
|
| Validation Efficiency |
|
| MGI Phenotype |
PHENOTYPE: Mice homozygous for a spontaneous nonsense mutation exhibit partial prenatal lethality, a hopping gait, preaxial polydactyly, male sterility due to lack of sperm flagella, impaired hearing, and patterning defects that are typical of impaired Hedgehog signaling. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 26 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 9230112D13Rik |
A |
T |
14: 34,233,898 (GRCm39) |
V131E |
unknown |
Het |
| Ccnk |
T |
C |
12: 108,168,647 (GRCm39) |
|
probably benign |
Het |
| Cd276 |
A |
G |
9: 58,444,603 (GRCm39) |
F123L |
probably benign |
Het |
| Ddr2 |
T |
A |
1: 169,825,730 (GRCm39) |
N290I |
probably damaging |
Het |
| Ecpas |
A |
G |
4: 58,828,622 (GRCm39) |
V937A |
possibly damaging |
Het |
| G530012D18Rik |
CAGAGAGA |
CAGAGAGAGA |
1: 85,504,945 (GRCm39) |
|
probably null |
Het |
| Gpt |
A |
G |
15: 76,582,666 (GRCm39) |
D37G |
probably damaging |
Het |
| Grik3 |
T |
A |
4: 125,564,437 (GRCm39) |
L473Q |
probably damaging |
Het |
| Hsp90b1 |
A |
C |
10: 86,539,349 (GRCm39) |
I90S |
probably damaging |
Het |
| Ing5 |
G |
A |
1: 93,731,710 (GRCm39) |
|
probably benign |
Het |
| Kalrn |
C |
T |
16: 33,810,180 (GRCm39) |
D2525N |
possibly damaging |
Het |
| Kdr |
T |
C |
5: 76,127,069 (GRCm39) |
Y307C |
probably damaging |
Het |
| Or51t4 |
A |
T |
7: 102,598,661 (GRCm39) |
M320L |
probably benign |
Het |
| Rapgef5 |
A |
G |
12: 117,677,854 (GRCm39) |
K161R |
probably damaging |
Het |
| Rassf10 |
A |
T |
7: 112,553,756 (GRCm39) |
D119V |
possibly damaging |
Het |
| Samhd1 |
A |
T |
2: 156,965,335 (GRCm39) |
F160Y |
possibly damaging |
Het |
| Sh3bp2 |
T |
A |
5: 34,700,900 (GRCm39) |
C34* |
probably null |
Het |
| Six3 |
A |
G |
17: 85,931,283 (GRCm39) |
E313G |
probably damaging |
Het |
| Tas2r118 |
A |
G |
6: 23,969,801 (GRCm39) |
F87L |
possibly damaging |
Het |
| Tmem131 |
A |
G |
1: 36,864,378 (GRCm39) |
L591P |
probably damaging |
Het |
| Trav17 |
A |
C |
14: 54,044,123 (GRCm39) |
S10R |
probably benign |
Het |
| Ttll3 |
T |
C |
6: 113,384,284 (GRCm39) |
F534S |
probably damaging |
Het |
| Umodl1 |
T |
A |
17: 31,211,147 (GRCm39) |
V890E |
probably damaging |
Het |
| Uso1 |
G |
A |
5: 92,343,294 (GRCm39) |
|
probably null |
Het |
| Utrn |
A |
G |
10: 12,519,172 (GRCm39) |
I2260T |
probably damaging |
Het |
| Vav1 |
A |
G |
17: 57,613,187 (GRCm39) |
N620D |
probably benign |
Het |
|
| Other mutations in Ift56 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00927:Ift56
|
APN |
6 |
38,359,155 (GRCm39) |
splice site |
probably benign |
|
|
IGL02049:Ift56
|
APN |
6 |
38,402,067 (GRCm39) |
missense |
probably benign |
0.16 |
|
IGL02403:Ift56
|
APN |
6 |
38,386,373 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
IGL02902:Ift56
|
APN |
6 |
38,402,097 (GRCm39) |
missense |
probably benign |
0.21 |
|
IGL03189:Ift56
|
APN |
6 |
38,402,166 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL03410:Ift56
|
APN |
6 |
38,362,435 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0346:Ift56
|
UTSW |
6 |
38,386,370 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0562:Ift56
|
UTSW |
6 |
38,378,064 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0826:Ift56
|
UTSW |
6 |
38,402,049 (GRCm39) |
splice site |
probably null |
|
|
R1212:Ift56
|
UTSW |
6 |
38,387,728 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1778:Ift56
|
UTSW |
6 |
38,386,411 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R1972:Ift56
|
UTSW |
6 |
38,387,738 (GRCm39) |
missense |
probably benign |
0.20 |
|
R2904:Ift56
|
UTSW |
6 |
38,378,037 (GRCm39) |
missense |
possibly damaging |
0.61 |
|
R2905:Ift56
|
UTSW |
6 |
38,378,037 (GRCm39) |
missense |
possibly damaging |
0.61 |
|
R3788:Ift56
|
UTSW |
6 |
38,380,459 (GRCm39) |
critical splice donor site |
probably null |
|
|
R4222:Ift56
|
UTSW |
6 |
38,372,010 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4392:Ift56
|
UTSW |
6 |
38,358,492 (GRCm39) |
start gained |
probably benign |
|
|
R4930:Ift56
|
UTSW |
6 |
38,368,475 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5484:Ift56
|
UTSW |
6 |
38,366,057 (GRCm39) |
missense |
probably benign |
0.10 |
|
R5920:Ift56
|
UTSW |
6 |
38,389,005 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6229:Ift56
|
UTSW |
6 |
38,371,975 (GRCm39) |
missense |
probably benign |
0.22 |
|
R6429:Ift56
|
UTSW |
6 |
38,375,248 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
R6901:Ift56
|
UTSW |
6 |
38,378,079 (GRCm39) |
missense |
possibly damaging |
0.80 |
|
R7448:Ift56
|
UTSW |
6 |
38,381,422 (GRCm39) |
nonsense |
probably null |
|
|
R7554:Ift56
|
UTSW |
6 |
38,362,435 (GRCm39) |
missense |
probably null |
1.00 |
|
R7650:Ift56
|
UTSW |
6 |
38,371,975 (GRCm39) |
missense |
probably benign |
0.22 |
|
R8319:Ift56
|
UTSW |
6 |
38,382,880 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R9270:Ift56
|
UTSW |
6 |
38,366,109 (GRCm39) |
intron |
probably benign |
|
|
R9417:Ift56
|
UTSW |
6 |
38,386,386 (GRCm39) |
missense |
probably damaging |
1.00 |
|
X0066:Ift56
|
UTSW |
6 |
38,382,877 (GRCm39) |
missense |
probably benign |
0.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- CTTGGTCTAGCCTTGGACTTAC -3'
(R):5'- AAGGCACAACTGGTAAGTGC -3'
Sequencing Primer
(F):5'- GGTCTAGCCTTGGACTTACTTGTTC -3'
(R):5'- GCACAACTGGTAAGTGCCATTC -3'
|
| Posted On |
2015-01-23 |
Incidental Mutation