Incidental Mutation 'R5593:Slc25a19'
| ID |
437644 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Slc25a19
|
| Ensembl Gene |
ENSMUSG00000020744 |
| Gene Name |
solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19 |
| Synonyms |
2900089E13Rik, DNC, MUP1, TPC |
| MMRRC Submission |
043145-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5593 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
115505004-115519121 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 115507418 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Asparagine
at position 235
(Y235N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000137534
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000021087]
[ENSMUST00000021089]
[ENSMUST00000106503]
[ENSMUST00000106506]
[ENSMUST00000106507]
[ENSMUST00000178003]
[ENSMUST00000135552]
[ENSMUST00000148574]
|
| AlphaFold |
Q9DAM5 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000021087
|
| SMART Domains |
Protein: ENSMUSP00000021087
Gene: ENSMUSG00000020743
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:MIF4G
|
4 |
205 |
1.4e-14 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000021089
AA Change: Y235N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000021089
Gene: ENSMUSG00000020744
AA Change: Y235N
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Mito_carr
|
12 |
111 |
5.7e-20 |
PFAM |
|
Pfam:Mito_carr
|
114 |
205 |
5.3e-24 |
PFAM |
|
Pfam:Mito_carr
|
212 |
313 |
5.2e-23 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000106503
AA Change: H173Q
PolyPhen 2
Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
|
| SMART Domains |
Protein: ENSMUSP00000102112
Gene: ENSMUSG00000020744
AA Change: H173Q
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Mito_carr
|
11 |
111 |
1.7e-22 |
PFAM |
|
Pfam:Mito_carr
|
114 |
172 |
9.7e-9 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000106506
|
| SMART Domains |
Protein: ENSMUSP00000102115
Gene: ENSMUSG00000020743
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:MIF4G
|
4 |
186 |
1.1e-9 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000106507
|
| SMART Domains |
Protein: ENSMUSP00000102116
Gene: ENSMUSG00000020743
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:MIF4G
|
4 |
204 |
3.5e-15 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000124407
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000127132
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129194
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000178003
AA Change: Y235N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000137534
Gene: ENSMUSG00000020744
AA Change: Y235N
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Mito_carr
|
11 |
111 |
1.1e-21 |
PFAM |
|
Pfam:Mito_carr
|
114 |
205 |
7e-25 |
PFAM |
|
Pfam:Mito_carr
|
212 |
313 |
1e-24 |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000135552
AA Change: Y152N
PolyPhen 2
Score 0.947 (Sensitivity: 0.79; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000114566
Gene: ENSMUSG00000020744
AA Change: Y152N
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Mito_carr
|
31 |
122 |
1.1e-25 |
PFAM |
|
Pfam:Mito_carr
|
129 |
226 |
4.7e-25 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000144083
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000139556
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000137304
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000146244
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000180919
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000142637
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000148574
|
| SMART Domains |
Protein: ENSMUSP00000119643
Gene: ENSMUSG00000020743
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:MIF4G
|
4 |
162 |
1.3e-7 |
PFAM |
|
| Meta Mutation Damage Score |
0.9438 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.7%
- 10x: 98.5%
- 20x: 95.9%
|
| Validation Efficiency |
100% (71/71) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a mitochondrial protein that is a member of the solute carrier family. Although this protein was initially thought to be the mitochondrial deoxynucleotide carrier involved in the uptake of deoxynucleotides into the matrix of the mitochondria, further studies have demonstrated that this protein instead functions as the mitochondrial thiamine pyrophosphate carrier, which transports thiamine pyrophosphates into mitochondria. Mutations in this gene cause microcephaly, Amish type, a metabolic disease that results in severe congenital microcephaly, severe 2-ketoglutaric aciduria, and death within the first year. Multiple alternatively spliced variants, encoding the same protein, have been identified for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutation of this gene results in lethality by E12, neural tube closure defects resulting in exencephaly and microcephaly, growth arrest, anemia, elevated alpha-ketoglutarate in amniotic fluid, and reduced thiamine pyrophosphate content in mitochondria. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 67 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930556J24Rik |
C |
T |
11: 3,888,027 (GRCm39) |
V120I |
unknown |
Het |
| Anpep |
T |
G |
7: 79,491,794 (GRCm39) |
K69T |
probably benign |
Het |
| Appbp2 |
A |
T |
11: 85,085,409 (GRCm39) |
I499K |
possibly damaging |
Het |
| Copb2 |
A |
G |
9: 98,469,091 (GRCm39) |
|
probably null |
Het |
| Cpa5 |
T |
C |
6: 30,630,848 (GRCm39) |
I370T |
probably benign |
Het |
| Cpn2 |
T |
C |
16: 30,078,898 (GRCm39) |
T268A |
probably benign |
Het |
| Ctbp2 |
C |
A |
7: 132,600,598 (GRCm39) |
R99I |
possibly damaging |
Het |
| Cul1 |
G |
A |
6: 47,462,020 (GRCm39) |
W196* |
probably null |
Het |
| Cul1 |
T |
C |
6: 47,491,925 (GRCm39) |
F402L |
probably damaging |
Het |
| Cysltr2 |
T |
C |
14: 73,266,931 (GRCm39) |
K260E |
probably benign |
Het |
| Dyrk1a |
C |
A |
16: 94,460,442 (GRCm39) |
Q33K |
possibly damaging |
Het |
| Elapor2 |
T |
A |
5: 9,316,350 (GRCm39) |
L27Q |
probably benign |
Het |
| Epg5 |
T |
A |
18: 78,000,689 (GRCm39) |
S542T |
probably damaging |
Het |
| Eps8l3 |
A |
T |
3: 107,798,504 (GRCm39) |
|
probably benign |
Het |
| Evc2 |
A |
G |
5: 37,544,321 (GRCm39) |
H690R |
probably damaging |
Het |
| Fam227a |
G |
A |
15: 79,524,259 (GRCm39) |
|
probably benign |
Het |
| Gadl1 |
G |
T |
9: 115,835,718 (GRCm39) |
G382V |
probably damaging |
Het |
| Gbf1 |
A |
G |
19: 46,260,963 (GRCm39) |
Q1176R |
possibly damaging |
Het |
| Gdf9 |
A |
T |
11: 53,324,558 (GRCm39) |
H109L |
probably damaging |
Het |
| Gsdmd |
T |
A |
15: 75,738,856 (GRCm39) |
V411D |
probably damaging |
Het |
| Hdc |
T |
C |
2: 126,460,504 (GRCm39) |
|
probably benign |
Het |
| Ifrd2 |
A |
G |
9: 107,467,374 (GRCm39) |
D82G |
probably damaging |
Het |
| Itpkb |
T |
C |
1: 180,161,661 (GRCm39) |
S596P |
probably damaging |
Het |
| Kcnmb3 |
A |
G |
3: 32,546,096 (GRCm39) |
V8A |
possibly damaging |
Het |
| Lyst |
T |
G |
13: 13,917,918 (GRCm39) |
I3326S |
probably damaging |
Het |
| Mcm9 |
G |
A |
10: 53,414,393 (GRCm39) |
T229I |
probably damaging |
Het |
| Medag |
T |
A |
5: 149,350,415 (GRCm39) |
F21L |
probably benign |
Het |
| Mefv |
A |
T |
16: 3,533,315 (GRCm39) |
C319S |
probably benign |
Het |
| Mettl23 |
T |
A |
11: 116,734,593 (GRCm39) |
V54D |
probably damaging |
Het |
| Mul1 |
A |
G |
4: 138,166,543 (GRCm39) |
D199G |
probably damaging |
Het |
| Ncor1 |
A |
T |
11: 62,260,130 (GRCm39) |
I266N |
probably damaging |
Het |
| Nek10 |
A |
T |
14: 14,980,544 (GRCm38) |
K967* |
probably null |
Het |
| Nrcam |
A |
G |
12: 44,606,483 (GRCm39) |
T410A |
probably damaging |
Het |
| Or1p1 |
A |
G |
11: 74,179,618 (GRCm39) |
I49V |
possibly damaging |
Het |
| Or2b11 |
T |
C |
11: 59,461,874 (GRCm39) |
R231G |
possibly damaging |
Het |
| Or52d13 |
C |
T |
7: 103,109,592 (GRCm39) |
|
silent |
Het |
| Or52e4 |
T |
C |
7: 104,705,711 (GRCm39) |
I86T |
probably damaging |
Het |
| Pate2 |
A |
T |
9: 35,581,778 (GRCm39) |
D24V |
possibly damaging |
Het |
| Plcb3 |
T |
C |
19: 6,932,117 (GRCm39) |
I1124V |
possibly damaging |
Het |
| Ptprc |
A |
T |
1: 138,045,458 (GRCm39) |
|
probably benign |
Het |
| Rab6a |
T |
C |
7: 100,257,378 (GRCm39) |
|
probably benign |
Het |
| Rnf208 |
G |
T |
2: 25,133,345 (GRCm39) |
W13L |
possibly damaging |
Het |
| Rps6kl1 |
G |
T |
12: 85,193,675 (GRCm39) |
Q139K |
possibly damaging |
Het |
| Sdk1 |
T |
A |
5: 141,941,879 (GRCm39) |
I509N |
probably damaging |
Het |
| Sephs1 |
A |
G |
2: 4,898,098 (GRCm39) |
I170V |
probably benign |
Het |
| Slc17a8 |
C |
T |
10: 89,442,702 (GRCm39) |
D44N |
probably benign |
Het |
| Slc23a1 |
T |
A |
18: 35,755,349 (GRCm39) |
I489F |
probably damaging |
Het |
| Slc47a2 |
A |
G |
11: 61,233,486 (GRCm39) |
V40A |
probably benign |
Het |
| Slurp2 |
C |
T |
15: 74,614,917 (GRCm39) |
V75I |
probably benign |
Het |
| Smc1b |
A |
C |
15: 85,005,842 (GRCm39) |
M354R |
probably benign |
Het |
| Spice1 |
C |
A |
16: 44,191,115 (GRCm39) |
A323E |
possibly damaging |
Het |
| Sptbn2 |
T |
A |
19: 4,798,975 (GRCm39) |
V2015E |
probably damaging |
Het |
| Sptlc2 |
A |
C |
12: 87,415,857 (GRCm39) |
F57V |
probably benign |
Het |
| Srsf1 |
A |
G |
11: 87,938,705 (GRCm39) |
N14S |
possibly damaging |
Het |
| Ssh2 |
T |
A |
11: 77,312,192 (GRCm39) |
D228E |
probably damaging |
Het |
| Synj2 |
A |
G |
17: 6,088,390 (GRCm39) |
*1480W |
probably null |
Het |
| Syt14 |
A |
T |
1: 192,613,231 (GRCm39) |
M523K |
probably damaging |
Het |
| Tff3 |
A |
T |
17: 31,348,516 (GRCm39) |
V12E |
probably benign |
Het |
| Tgm2 |
C |
A |
2: 157,969,262 (GRCm39) |
C371F |
probably damaging |
Het |
| Tmem260 |
A |
C |
14: 48,711,501 (GRCm39) |
I197L |
probably benign |
Het |
| Unc5a |
A |
G |
13: 55,152,747 (GRCm39) |
D887G |
possibly damaging |
Het |
| Vstm4 |
G |
T |
14: 32,641,247 (GRCm39) |
A277S |
probably benign |
Het |
| Wdtc1 |
A |
T |
4: 133,021,702 (GRCm39) |
|
probably null |
Het |
| Zan |
A |
G |
5: 137,466,600 (GRCm39) |
F419S |
possibly damaging |
Het |
| Zfp317 |
G |
A |
9: 19,558,584 (GRCm39) |
R266Q |
probably damaging |
Het |
| Zfp931 |
T |
A |
2: 177,709,595 (GRCm39) |
T264S |
possibly damaging |
Het |
| Zpld2 |
T |
C |
4: 133,920,350 (GRCm39) |
K605R |
probably damaging |
Het |
|
| Other mutations in Slc25a19 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
Baggins
|
UTSW |
11 |
115,508,386 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
rings
|
UTSW |
11 |
115,506,377 (GRCm39) |
missense |
probably benign |
0.14 |
|
BB001:Slc25a19
|
UTSW |
11 |
115,506,376 (GRCm39) |
missense |
unknown |
|
|
BB011:Slc25a19
|
UTSW |
11 |
115,506,376 (GRCm39) |
missense |
unknown |
|
|
PIT4498001:Slc25a19
|
UTSW |
11 |
115,514,781 (GRCm39) |
missense |
possibly damaging |
0.80 |
|
R0335:Slc25a19
|
UTSW |
11 |
115,515,032 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0398:Slc25a19
|
UTSW |
11 |
115,508,401 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0454:Slc25a19
|
UTSW |
11 |
115,508,423 (GRCm39) |
nonsense |
probably null |
|
|
R1614:Slc25a19
|
UTSW |
11 |
115,507,449 (GRCm39) |
nonsense |
probably null |
|
|
R3775:Slc25a19
|
UTSW |
11 |
115,506,285 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3776:Slc25a19
|
UTSW |
11 |
115,506,285 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5000:Slc25a19
|
UTSW |
11 |
115,507,497 (GRCm39) |
splice site |
probably null |
|
|
R5738:Slc25a19
|
UTSW |
11 |
115,515,060 (GRCm39) |
missense |
probably benign |
0.24 |
|
R6167:Slc25a19
|
UTSW |
11 |
115,506,377 (GRCm39) |
missense |
probably benign |
0.14 |
|
R6306:Slc25a19
|
UTSW |
11 |
115,508,386 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R7014:Slc25a19
|
UTSW |
11 |
115,511,792 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7161:Slc25a19
|
UTSW |
11 |
115,507,373 (GRCm39) |
missense |
possibly damaging |
0.66 |
|
R7924:Slc25a19
|
UTSW |
11 |
115,506,376 (GRCm39) |
missense |
unknown |
|
|
| Predicted Primers |
PCR Primer
(F):5'- TGCAGGTGTGTTTATGCACA -3'
(R):5'- CACAGTGATGTGCTGGCTAA -3'
Sequencing Primer
(F):5'- GTGTTTATGCACAGAAATAAAGCTAC -3'
(R):5'- CAAGCAATTGTGAGCTGTCTGAC -3'
|
| Posted On |
2016-10-26 |
Incidental Mutation