Incidental Mutation 'R4019:Spdya'
| ID |
312709 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Spdya
|
| Ensembl Gene |
ENSMUSG00000052525 |
| Gene Name |
speedy/RINGO cell cycle regulator family, member A |
| Synonyms |
speedy A1, speedy/ringo, Spdy1, 4921517J08Rik, 4930548B21Rik, speedy A2 |
| MMRRC Submission |
040953-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.387)
|
| Stock # |
R4019 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
17 |
| Chromosomal Location |
71859056-71896528 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to C
at 71863309 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Lysine to Asparagine
at position 19
(K19N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000125912
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000064420]
[ENSMUST00000124001]
[ENSMUST00000144142]
[ENSMUST00000167641]
|
| AlphaFold |
Q5IBH7 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000064420
AA Change: K19N
PolyPhen 2
Score 0.718 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000063214
Gene: ENSMUSG00000052525
AA Change: K19N
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Spy1
|
68 |
198 |
8.2e-63 |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000124001
AA Change: K19N
PolyPhen 2
Score 0.718 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000118426
Gene: ENSMUSG00000052525
AA Change: K19N
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Spy1
|
68 |
198 |
1.5e-69 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130218
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130952
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000137830
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000144142
AA Change: K19N
PolyPhen 2
Score 0.718 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000118994
Gene: ENSMUSG00000052525
AA Change: K19N
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Spy1
|
68 |
198 |
2.2e-62 |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000167641
AA Change: K19N
PolyPhen 2
Score 0.718 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000125912
Gene: ENSMUSG00000052525
AA Change: K19N
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Spy1
|
68 |
198 |
5.1e-69 |
PFAM |
|
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 97.0%
- 20x: 94.2%
|
| Validation Efficiency |
|
| MGI Phenotype |
PHENOTYPE: Homozygous inactivation of this gene results in impaired telomere attachment to the nuclear envelope during early meiosis, abnormal chromosome pairing and homologous synapsis, and meiotic prophase I arrest in male and female germ cells leading to infertility in both sexes. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 43 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acy1 |
T |
C |
9: 106,313,978 (GRCm39) |
T61A |
possibly damaging |
Het |
| Ap4e1 |
C |
T |
2: 126,903,846 (GRCm39) |
S916F |
probably benign |
Het |
| Brpf1 |
G |
A |
6: 113,287,243 (GRCm39) |
R157Q |
probably damaging |
Het |
| Canx |
A |
T |
11: 50,190,072 (GRCm39) |
S429T |
probably damaging |
Het |
| Casz1 |
C |
T |
4: 149,017,335 (GRCm39) |
P208L |
probably benign |
Het |
| Ctnnd1 |
C |
T |
2: 84,450,302 (GRCm39) |
R306H |
probably damaging |
Het |
| Dip2c |
T |
C |
13: 9,664,401 (GRCm39) |
V909A |
probably damaging |
Het |
| Epg5 |
C |
A |
18: 78,073,665 (GRCm39) |
Q2511K |
probably damaging |
Het |
| Ghitm |
G |
A |
14: 36,852,651 (GRCm39) |
A143V |
probably damaging |
Het |
| Gramd2b |
T |
C |
18: 56,612,026 (GRCm39) |
|
probably null |
Het |
| Ifitm3 |
T |
C |
7: 140,589,772 (GRCm39) |
T94A |
possibly damaging |
Het |
| Ift81 |
G |
A |
5: 122,731,192 (GRCm39) |
T321M |
probably benign |
Het |
| Ikbkb |
C |
T |
8: 23,161,728 (GRCm39) |
V387I |
probably benign |
Het |
| Lct |
T |
C |
1: 128,231,963 (GRCm39) |
M629V |
probably damaging |
Het |
| Lpar5 |
A |
G |
6: 125,058,638 (GRCm39) |
N120D |
probably damaging |
Het |
| Lrrc37 |
A |
G |
11: 103,506,119 (GRCm39) |
S1950P |
probably benign |
Het |
| Lrrtm2 |
T |
C |
18: 35,345,923 (GRCm39) |
I460V |
possibly damaging |
Het |
| Naip5 |
T |
C |
13: 100,359,883 (GRCm39) |
E451G |
probably benign |
Het |
| Naip5 |
T |
C |
13: 100,359,902 (GRCm39) |
I445V |
probably benign |
Het |
| Nbas |
A |
G |
12: 13,532,520 (GRCm39) |
R1743G |
probably damaging |
Het |
| Nherf4 |
A |
T |
9: 44,162,117 (GRCm39) |
|
probably null |
Het |
| Notch1 |
T |
C |
2: 26,371,154 (GRCm39) |
T311A |
probably benign |
Het |
| Oplah |
A |
G |
15: 76,181,476 (GRCm39) |
Y1155H |
probably damaging |
Het |
| Or4c15 |
A |
G |
2: 88,760,080 (GRCm39) |
I193T |
probably benign |
Het |
| Or52k2 |
T |
C |
7: 102,253,849 (GRCm39) |
F96S |
probably damaging |
Het |
| Pcnx1 |
C |
T |
12: 81,965,018 (GRCm39) |
T395I |
probably damaging |
Het |
| Pdgfb |
A |
C |
15: 79,885,923 (GRCm39) |
V108G |
probably damaging |
Het |
| Prpf40b |
T |
C |
15: 99,214,357 (GRCm39) |
S846P |
probably benign |
Het |
| Ptprc |
T |
A |
1: 138,006,254 (GRCm39) |
H752L |
probably damaging |
Het |
| Rin2 |
C |
T |
2: 145,702,366 (GRCm39) |
T354I |
probably benign |
Het |
| Scn3a |
A |
G |
2: 65,356,295 (GRCm39) |
|
probably benign |
Het |
| Sco1 |
T |
G |
11: 66,954,846 (GRCm39) |
S284A |
probably benign |
Het |
| Slc25a10 |
T |
A |
11: 120,388,265 (GRCm39) |
M227K |
probably damaging |
Het |
| Sox8 |
A |
G |
17: 25,789,271 (GRCm39) |
Y76H |
probably damaging |
Het |
| Syngap1 |
C |
T |
17: 27,171,315 (GRCm39) |
|
probably benign |
Het |
| Sytl3 |
T |
C |
17: 7,003,892 (GRCm39) |
S326P |
probably damaging |
Het |
| Tbl3 |
A |
G |
17: 24,923,695 (GRCm39) |
V239A |
probably damaging |
Het |
| Tenm2 |
T |
C |
11: 35,937,901 (GRCm39) |
I1592V |
probably benign |
Het |
| Vmn2r109 |
T |
A |
17: 20,774,074 (GRCm39) |
D427V |
probably benign |
Het |
| Vmn2r115 |
A |
G |
17: 23,579,017 (GRCm39) |
K830R |
probably damaging |
Het |
| Vmn2r45 |
A |
T |
7: 8,474,580 (GRCm39) |
L816* |
probably null |
Het |
| Zfp335 |
C |
T |
2: 164,743,380 (GRCm39) |
R536H |
probably damaging |
Het |
| Zfp777 |
T |
A |
6: 48,019,046 (GRCm39) |
Q296L |
probably damaging |
Het |
|
| Other mutations in Spdya |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01065:Spdya
|
APN |
17 |
71,863,320 (GRCm39) |
missense |
possibly damaging |
0.51 |
|
IGL01667:Spdya
|
APN |
17 |
71,863,254 (GRCm39) |
start codon destroyed |
probably null |
1.00 |
|
IGL02103:Spdya
|
APN |
17 |
71,885,242 (GRCm39) |
missense |
probably benign |
0.15 |
|
IGL02934:Spdya
|
APN |
17 |
71,863,395 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL03220:Spdya
|
APN |
17 |
71,885,286 (GRCm39) |
missense |
possibly damaging |
0.87 |
|
R0143:Spdya
|
UTSW |
17 |
71,865,635 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R0570:Spdya
|
UTSW |
17 |
71,869,585 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1666:Spdya
|
UTSW |
17 |
71,885,235 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4224:Spdya
|
UTSW |
17 |
71,869,519 (GRCm39) |
missense |
probably benign |
0.07 |
|
R4225:Spdya
|
UTSW |
17 |
71,869,519 (GRCm39) |
missense |
probably benign |
0.07 |
|
R4663:Spdya
|
UTSW |
17 |
71,885,339 (GRCm39) |
missense |
probably benign |
0.04 |
|
R5013:Spdya
|
UTSW |
17 |
71,869,499 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R5038:Spdya
|
UTSW |
17 |
71,895,561 (GRCm39) |
intron |
probably benign |
|
|
R5583:Spdya
|
UTSW |
17 |
71,876,126 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8323:Spdya
|
UTSW |
17 |
71,895,587 (GRCm39) |
missense |
probably benign |
0.39 |
|
R9664:Spdya
|
UTSW |
17 |
71,869,513 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- GAGCAGTTTCTAACATGATCCAG -3'
(R):5'- ATGTGTGCATTCCCCAACC -3'
Sequencing Primer
(F):5'- CAGTTTCTAACATGATCCAGTGTTAC -3'
(R):5'- GCTAGACTAACAAAATGTTTTACACC -3'
|
| Posted On |
2015-04-30 |
Incidental Mutation