Incidental Mutation 'PIT4498001:Slc25a19'
| ID |
556071 |
| 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 |
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
PIT4498001 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
11 |
| Chromosomal Location |
115505004-115519121 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 115514781 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Valine
at position 69
(I69V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000021089
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000021089]
[ENSMUST00000106503]
[ENSMUST00000135552]
[ENSMUST00000141614]
[ENSMUST00000154623]
[ENSMUST00000155709]
[ENSMUST00000178003]
|
| AlphaFold |
Q9DAM5 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000021089
AA Change: I69V
PolyPhen 2
Score 0.795 (Sensitivity: 0.85; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000021089
Gene: ENSMUSG00000020744
AA Change: I69V
| 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 damaging
Transcript: ENSMUST00000106503
AA Change: I69V
PolyPhen 2
Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000102112
Gene: ENSMUSG00000020744
AA Change: I69V
| 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: ENSMUST00000135552
|
| SMART Domains |
Protein: ENSMUSP00000114566
Gene: ENSMUSG00000020744
| 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 |
probably benign
Transcript: ENSMUST00000141614
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000154623
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000155709
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000178003
AA Change: I69V
PolyPhen 2
Score 0.795 (Sensitivity: 0.85; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000137534
Gene: ENSMUSG00000020744
AA Change: I69V
| 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 |
|
| Coding Region Coverage |
- 1x: 93.2%
- 3x: 91.0%
- 10x: 86.1%
- 20x: 75.4%
|
| Validation Efficiency |
|
| 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: 40 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aldh18a1 |
T |
C |
19: 40,562,800 (GRCm39) |
N191S |
probably benign |
Het |
| Cacnb2 |
T |
A |
2: 14,879,630 (GRCm39) |
L84* |
probably null |
Het |
| Cdhr2 |
C |
T |
13: 54,866,052 (GRCm39) |
T284M |
possibly damaging |
Het |
| Defb45 |
T |
C |
2: 152,438,394 (GRCm39) |
|
probably benign |
Het |
| Dkk3 |
C |
T |
7: 111,718,679 (GRCm39) |
V236M |
probably benign |
Het |
| Dscc1 |
A |
T |
15: 54,945,711 (GRCm39) |
V328D |
probably benign |
Het |
| Epha3 |
T |
C |
16: 63,372,889 (GRCm39) |
Y938C |
probably damaging |
Het |
| Erc1 |
A |
T |
6: 119,756,452 (GRCm39) |
F435I |
possibly damaging |
Het |
| Fbxl5 |
T |
C |
5: 43,908,323 (GRCm39) |
Y626C |
possibly damaging |
Het |
| Fmn2 |
A |
G |
1: 174,440,170 (GRCm39) |
R1196G |
probably damaging |
Het |
| Gabrr1 |
C |
T |
4: 33,160,225 (GRCm39) |
S303F |
probably damaging |
Het |
| Ggt1 |
T |
C |
10: 75,414,689 (GRCm39) |
V169A |
possibly damaging |
Het |
| Gm10800 |
CAAGAAAACTGAAAATCAAAGAAAACTGAAAATCA |
CAAGAAAACTGAAAATCA |
2: 98,497,361 (GRCm39) |
|
probably null |
Het |
| Gm3182 |
T |
A |
14: 4,481,832 (GRCm38) |
C9S |
probably damaging |
Het |
| Gpr88 |
A |
C |
3: 116,046,264 (GRCm39) |
S16A |
unknown |
Het |
| Kalrn |
A |
T |
16: 33,851,952 (GRCm39) |
M2076K |
possibly damaging |
Het |
| Katnip |
A |
G |
7: 125,412,768 (GRCm39) |
T371A |
probably benign |
Het |
| Kcnd3 |
T |
C |
3: 105,566,025 (GRCm39) |
I402T |
probably damaging |
Het |
| Mink1 |
A |
G |
11: 70,489,714 (GRCm39) |
D57G |
probably benign |
Het |
| Ncl |
T |
C |
1: 86,279,162 (GRCm39) |
T584A |
possibly damaging |
Het |
| Nfx1 |
A |
T |
4: 40,977,244 (GRCm39) |
Q306L |
probably benign |
Het |
| Ogdh |
A |
T |
11: 6,290,504 (GRCm39) |
D374V |
probably benign |
Het |
| Or5d39 |
T |
A |
2: 87,980,259 (GRCm39) |
T35S |
probably benign |
Het |
| Pak5 |
T |
A |
2: 135,925,211 (GRCm39) |
H697L |
probably damaging |
Het |
| Pappa |
T |
C |
4: 65,234,469 (GRCm39) |
C1425R |
probably damaging |
Het |
| Pramel26 |
T |
C |
4: 143,539,406 (GRCm39) |
E29G |
possibly damaging |
Het |
| Rab3gap2 |
T |
A |
1: 185,013,882 (GRCm39) |
I1196N |
probably damaging |
Het |
| Ralyl |
A |
T |
3: 14,172,299 (GRCm39) |
D56V |
probably damaging |
Het |
| Scin |
C |
T |
12: 40,119,446 (GRCm39) |
|
probably null |
Het |
| Slc8a1 |
G |
T |
17: 81,956,269 (GRCm39) |
Y256* |
probably null |
Het |
| Smyd1 |
T |
C |
6: 71,196,272 (GRCm39) |
H372R |
probably benign |
Het |
| St8sia1 |
T |
C |
6: 142,859,848 (GRCm39) |
T94A |
probably damaging |
Het |
| Stard9 |
T |
A |
2: 120,527,916 (GRCm39) |
M1391K |
possibly damaging |
Het |
| Tlr9 |
G |
A |
9: 106,100,721 (GRCm39) |
R4H |
probably benign |
Het |
| Trim50 |
A |
G |
5: 135,382,331 (GRCm39) |
D61G |
probably damaging |
Het |
| Ttn |
G |
A |
2: 76,597,295 (GRCm39) |
P19873S |
probably damaging |
Het |
| Vmn1r228 |
G |
T |
17: 20,996,772 (GRCm39) |
H249N |
probably benign |
Het |
| Vmn2r108 |
C |
T |
17: 20,683,279 (GRCm39) |
G642S |
probably damaging |
Het |
| Wdr27 |
A |
G |
17: 15,154,831 (GRCm39) |
S29P |
probably benign |
Het |
| Zan |
A |
G |
5: 137,415,298 (GRCm39) |
|
probably null |
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 |
|
|
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 |
|
|
R5593:Slc25a19
|
UTSW |
11 |
115,507,418 (GRCm39) |
missense |
probably damaging |
1.00 |
|
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'- ATCTCCCATGAAGGCAAACTG -3'
(R):5'- TTAGTCCCAGCAAAGGCAGTC -3'
Sequencing Primer
(F):5'- AACTGGCAGAGTGGGGCTTG -3'
(R):5'- GGCAGTCCCCAAAACTTAGAATTCTG -3'
|
| Posted On |
2019-06-07 |
Incidental Mutation