Incidental Mutation 'R6429:Ift56'
| ID |
518424 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ift56
|
| Ensembl Gene |
ENSMUSG00000056832 |
| Gene Name |
intraflagellar transport 56 |
| Synonyms |
hpy, hydrocephalic-polydactyl, 9430097H08Rik, hop, Ttc26 |
| MMRRC Submission |
044567-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.583)
|
| Stock # |
R6429 (G1)
|
| Quality Score |
223.009 |
|
Status
|
Not validated
|
| Chromosome |
6 |
| Chromosomal Location |
38358404-38404582 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 38375248 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Threonine
at position 250
(S250T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000124369
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000159145]
[ENSMUST00000160215]
[ENSMUST00000161751]
[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 |
probably benign
Transcript: ENSMUST00000161751
|
| SMART Domains |
Protein: ENSMUSP00000124271
Gene: ENSMUSG00000056832
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
19 |
29 |
N/A |
INTRINSIC |
|
Pfam:TPR_2
|
58 |
88 |
1.3e-5 |
PFAM |
|
Pfam:TPR_8
|
58 |
91 |
1.8e-3 |
PFAM |
|
Pfam:TPR_6
|
59 |
87 |
2.6e-3 |
PFAM |
|
Pfam:TPR_1
|
61 |
87 |
4.8e-4 |
PFAM |
|
Pfam:TPR_11
|
63 |
115 |
4.1e-11 |
PFAM |
|
Pfam:TPR_19
|
67 |
130 |
1.7e-7 |
PFAM |
|
Pfam:TPR_8
|
89 |
113 |
2.1e-3 |
PFAM |
|
Pfam:TPR_1
|
91 |
113 |
1.8e-4 |
PFAM |
|
Pfam:TPR_2
|
91 |
113 |
2.5e-3 |
PFAM |
|
Pfam:TPR_9
|
145 |
210 |
9.4e-4 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000162486
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000162554
AA Change: S250T
PolyPhen 2
Score 0.692 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000124369
Gene: ENSMUSG00000056832
AA Change: S250T
| 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
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.5%
- 10x: 97.6%
- 20x: 92.6%
|
| 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: 53 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acacb |
G |
A |
5: 114,366,652 (GRCm39) |
E1565K |
probably damaging |
Het |
| Amy1 |
T |
C |
3: 113,363,158 (GRCm39) |
N63S |
probably damaging |
Het |
| Arhgef15 |
G |
T |
11: 68,838,622 (GRCm39) |
N591K |
probably damaging |
Het |
| AW551984 |
A |
G |
9: 39,511,910 (GRCm39) |
S34P |
probably damaging |
Het |
| C2cd3 |
A |
G |
7: 100,081,298 (GRCm39) |
D127G |
probably damaging |
Het |
| Ccdc87 |
T |
A |
19: 4,891,263 (GRCm39) |
V585E |
probably benign |
Het |
| Cemip2 |
T |
C |
19: 21,779,272 (GRCm39) |
C361R |
probably benign |
Het |
| Cul2 |
T |
C |
18: 3,421,345 (GRCm39) |
I223T |
probably damaging |
Het |
| Dgkq |
C |
T |
5: 108,801,574 (GRCm39) |
V495M |
probably damaging |
Het |
| Dpp10 |
A |
G |
1: 123,295,330 (GRCm39) |
I570T |
possibly damaging |
Het |
| Dstyk |
C |
T |
1: 132,377,542 (GRCm39) |
Q383* |
probably null |
Het |
| Emilin2 |
C |
A |
17: 71,617,951 (GRCm39) |
|
probably benign |
Het |
| Fnip1 |
A |
G |
11: 54,406,393 (GRCm39) |
I1163M |
probably damaging |
Het |
| Fryl |
C |
T |
5: 73,248,094 (GRCm39) |
E1008K |
possibly damaging |
Het |
| Gm35315 |
A |
T |
5: 110,226,525 (GRCm39) |
Y305N |
possibly damaging |
Het |
| Grhl3 |
T |
A |
4: 135,284,507 (GRCm39) |
D195V |
probably damaging |
Het |
| Il33 |
T |
C |
19: 29,929,400 (GRCm39) |
F41S |
probably benign |
Het |
| Il4 |
A |
G |
11: 53,504,736 (GRCm39) |
S15P |
possibly damaging |
Het |
| Inf2 |
C |
T |
12: 112,570,690 (GRCm39) |
P410S |
probably benign |
Het |
| Kalrn |
T |
A |
16: 34,152,534 (GRCm39) |
D349V |
possibly damaging |
Het |
| Krt4 |
A |
G |
15: 101,831,229 (GRCm39) |
M224T |
probably benign |
Het |
| Lrp2 |
C |
T |
2: 69,291,631 (GRCm39) |
S3516N |
probably damaging |
Het |
| Macf1 |
A |
T |
4: 123,295,387 (GRCm39) |
|
probably null |
Het |
| Msr1 |
G |
A |
8: 40,068,858 (GRCm39) |
P213S |
probably damaging |
Het |
| Nptx1 |
G |
T |
11: 119,435,547 (GRCm39) |
C256* |
probably null |
Het |
| Nr1d1 |
T |
C |
11: 98,662,840 (GRCm39) |
Y51C |
probably damaging |
Het |
| Or4c11c |
G |
A |
2: 88,661,869 (GRCm39) |
R136Q |
probably benign |
Het |
| Panx3 |
T |
C |
9: 37,572,461 (GRCm39) |
D363G |
probably damaging |
Het |
| Pira13 |
A |
T |
7: 3,825,345 (GRCm39) |
H432Q |
possibly damaging |
Het |
| Prkag1 |
A |
G |
15: 98,712,404 (GRCm39) |
F143L |
probably damaging |
Het |
| Ptger4 |
T |
C |
15: 5,272,478 (GRCm39) |
K72R |
possibly damaging |
Het |
| Pvrig-ps |
A |
G |
5: 138,340,312 (GRCm39) |
T28A |
probably benign |
Het |
| Rhod |
C |
T |
19: 4,476,133 (GRCm39) |
C206Y |
probably benign |
Het |
| Rngtt |
C |
A |
4: 33,320,606 (GRCm39) |
S51* |
probably null |
Het |
| Rreb1 |
T |
G |
13: 38,116,105 (GRCm39) |
S1155A |
probably benign |
Het |
| Scn9a |
A |
C |
2: 66,357,307 (GRCm39) |
I998S |
possibly damaging |
Het |
| Sfmbt1 |
T |
A |
14: 30,495,868 (GRCm39) |
F50L |
probably damaging |
Het |
| Six4 |
A |
T |
12: 73,150,247 (GRCm39) |
V766D |
probably damaging |
Het |
| Smpd1 |
T |
C |
7: 105,206,135 (GRCm39) |
I421T |
probably damaging |
Het |
| Son |
T |
A |
16: 91,455,054 (GRCm39) |
M1267K |
probably benign |
Het |
| Styk1 |
T |
A |
6: 131,287,027 (GRCm39) |
D156V |
possibly damaging |
Het |
| Supt3 |
A |
G |
17: 45,430,030 (GRCm39) |
E361G |
probably benign |
Het |
| Tbx3 |
T |
A |
5: 119,812,256 (GRCm39) |
Y185* |
probably null |
Het |
| Trpm1 |
A |
T |
7: 63,918,252 (GRCm39) |
T531S |
probably benign |
Het |
| Tspan32 |
T |
A |
7: 142,572,479 (GRCm39) |
W172R |
possibly damaging |
Het |
| Urb1 |
A |
T |
16: 90,559,318 (GRCm39) |
|
probably null |
Het |
| Vmn2r70 |
T |
A |
7: 85,208,276 (GRCm39) |
I734F |
probably damaging |
Het |
| Vwa7 |
A |
G |
17: 35,243,175 (GRCm39) |
T618A |
probably benign |
Het |
| Wac |
T |
A |
18: 7,920,163 (GRCm39) |
V339E |
probably damaging |
Het |
| Wrn |
G |
A |
8: 33,833,024 (GRCm39) |
T156M |
probably damaging |
Het |
| Zeb1 |
T |
A |
18: 5,770,498 (GRCm39) |
C884S |
probably damaging |
Het |
| Zfp747l1 |
T |
C |
7: 126,984,214 (GRCm39) |
|
probably benign |
Het |
| Zmpste24 |
A |
G |
4: 120,952,867 (GRCm39) |
V10A |
probably damaging |
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 |
|
R2903:Ift56
|
UTSW |
6 |
38,378,037 (GRCm39) |
missense |
possibly damaging |
0.61 |
|
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 |
|
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'- ATTCAGAAACCCGGAGCTG -3'
(R):5'- ATCTCTACCACAGGAAGGCAG -3'
Sequencing Primer
(F):5'- AGTTCTCAGCAACAGTGTGC -3'
(R):5'- AGGAAGGCAGCACTCCCTG -3'
|
| Posted On |
2018-05-24 |
Incidental Mutation