Incidental Mutation 'R0107:Mthfd1l'
| ID |
33337 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Mthfd1l
|
| Ensembl Gene |
ENSMUSG00000040675 |
| Gene Name |
methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like |
| Synonyms |
2410004L15Rik, Fthfsdc1 |
| MMRRC Submission |
038393-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R0107 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
10 |
| Chromosomal Location |
3923118-4117081 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 3991838 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Histidine
at position 597
(Y597H)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000112897
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000043735]
[ENSMUST00000117291]
[ENSMUST00000120585]
|
| AlphaFold |
Q3V3R1 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000043735
AA Change: Y597H
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000036178
Gene: ENSMUSG00000040675
AA Change: Y597H
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
4 |
18 |
N/A |
INTRINSIC |
|
low complexity region
|
30 |
41 |
N/A |
INTRINSIC |
|
Pfam:THF_DHG_CYH
|
71 |
179 |
2.9e-15 |
PFAM |
|
Pfam:THF_DHG_CYH_C
|
182 |
337 |
1.1e-27 |
PFAM |
|
Pfam:FTHFS
|
358 |
977 |
1.2e-260 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000117291
AA Change: Y597H
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000112870
Gene: ENSMUSG00000040675
AA Change: Y597H
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
4 |
18 |
N/A |
INTRINSIC |
|
low complexity region
|
30 |
41 |
N/A |
INTRINSIC |
|
Pfam:THF_DHG_CYH
|
71 |
179 |
2.9e-15 |
PFAM |
|
Pfam:THF_DHG_CYH_C
|
182 |
337 |
1.1e-27 |
PFAM |
|
Pfam:FTHFS
|
358 |
977 |
1.2e-260 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000120585
AA Change: Y597H
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000112897
Gene: ENSMUSG00000040675
AA Change: Y597H
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
4 |
18 |
N/A |
INTRINSIC |
|
low complexity region
|
30 |
41 |
N/A |
INTRINSIC |
|
Pfam:THF_DHG_CYH
|
70 |
179 |
8e-17 |
PFAM |
|
Pfam:THF_DHG_CYH_C
|
182 |
337 |
5.4e-28 |
PFAM |
|
Pfam:FTHFS
|
359 |
977 |
7.2e-260 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000154517
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.0%
- 3x: 98.1%
- 10x: 95.8%
- 20x: 90.6%
|
| Validation Efficiency |
99% (71/72) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is involved in the synthesis of tetrahydrofolate (THF) in the mitochondrion. THF is important in the de novo synthesis of purines and thymidylate and in the regeneration of methionine from homocysteine. Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jun 2011]
PHENOTYPE: Homozygous deletion of this gene causes embryonic lethality, delayed embryonic growth, craniofacial anomalies, and neural tube defects including craniorachischisis, exencephaly and/or a wavy neural tube. Maternal formate supplementation reduces the incidence of NTDs and improves embryonic growth. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 63 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aadacl2fm2 |
T |
A |
3: 59,659,737 (GRCm39) |
L397I |
possibly damaging |
Het |
| Abca1 |
A |
G |
4: 53,080,834 (GRCm39) |
V825A |
probably benign |
Het |
| Adamts7 |
T |
C |
9: 90,062,773 (GRCm39) |
I409T |
possibly damaging |
Het |
| Adck1 |
T |
C |
12: 88,413,426 (GRCm39) |
W253R |
possibly damaging |
Het |
| Afg3l2 |
A |
G |
18: 67,564,836 (GRCm39) |
F213L |
probably damaging |
Het |
| Ankle2 |
T |
C |
5: 110,400,893 (GRCm39) |
V743A |
probably benign |
Het |
| Ankrd34c |
C |
T |
9: 89,611,537 (GRCm39) |
R268H |
probably benign |
Het |
| Arb2a |
A |
G |
13: 78,050,933 (GRCm39) |
D145G |
probably damaging |
Het |
| Bcl2 |
G |
A |
1: 106,640,292 (GRCm39) |
R107C |
probably damaging |
Het |
| Ccdc7b |
T |
G |
8: 129,904,678 (GRCm39) |
|
probably benign |
Het |
| Cd320 |
A |
T |
17: 34,067,059 (GRCm39) |
M169L |
probably benign |
Het |
| Chn1 |
A |
G |
2: 73,445,028 (GRCm39) |
Y338H |
probably damaging |
Het |
| Chuk |
T |
A |
19: 44,085,358 (GRCm39) |
S263C |
probably damaging |
Het |
| Dennd4b |
C |
A |
3: 90,180,043 (GRCm39) |
P663T |
possibly damaging |
Het |
| Dnajc24 |
T |
G |
2: 105,832,259 (GRCm39) |
|
probably benign |
Het |
| Fbn2 |
A |
G |
18: 58,189,275 (GRCm39) |
V1617A |
probably benign |
Het |
| Fermt2 |
T |
C |
14: 45,702,279 (GRCm39) |
N502D |
probably damaging |
Het |
| Frrs1 |
A |
T |
3: 116,690,365 (GRCm39) |
I3F |
probably damaging |
Het |
| Fut1 |
C |
A |
7: 45,268,270 (GRCm39) |
Q20K |
possibly damaging |
Het |
| Gbf1 |
T |
C |
19: 46,273,267 (GRCm39) |
V1709A |
probably benign |
Het |
| Gfra3 |
G |
T |
18: 34,844,359 (GRCm39) |
H60Q |
probably benign |
Het |
| Gm10750 |
T |
A |
2: 148,857,973 (GRCm39) |
M93L |
unknown |
Het |
| Hmcn1 |
T |
A |
1: 150,462,766 (GRCm39) |
I5124L |
probably benign |
Het |
| Hps3 |
A |
C |
3: 20,084,960 (GRCm39) |
L76R |
probably damaging |
Het |
| Ifrd1 |
T |
A |
12: 40,264,080 (GRCm39) |
Q105L |
probably damaging |
Het |
| Irs2 |
A |
T |
8: 11,054,691 (GRCm39) |
V1247E |
probably damaging |
Het |
| Itgal |
T |
C |
7: 126,927,731 (GRCm39) |
|
probably benign |
Het |
| Ivns1abp |
A |
T |
1: 151,237,321 (GRCm39) |
N495I |
probably damaging |
Het |
| Kank1 |
T |
A |
19: 25,407,730 (GRCm39) |
|
probably benign |
Het |
| Mroh8 |
T |
C |
2: 157,067,388 (GRCm39) |
Q657R |
probably benign |
Het |
| Myom1 |
G |
A |
17: 71,384,360 (GRCm39) |
V692I |
probably damaging |
Het |
| Or13a17 |
A |
T |
7: 140,271,258 (GRCm39) |
M147L |
probably benign |
Het |
| Or1j18 |
T |
G |
2: 36,624,730 (GRCm39) |
Y132* |
probably null |
Het |
| Or7g20 |
A |
G |
9: 18,946,629 (GRCm39) |
D70G |
probably damaging |
Het |
| Palmd |
A |
T |
3: 116,717,725 (GRCm39) |
H257Q |
probably damaging |
Het |
| Pcnx2 |
A |
T |
8: 126,480,325 (GRCm39) |
V1994D |
probably benign |
Het |
| Phkb |
G |
A |
8: 86,743,560 (GRCm39) |
G553S |
probably benign |
Het |
| Plekha5 |
G |
A |
6: 140,537,473 (GRCm39) |
R646K |
possibly damaging |
Het |
| Ptprn |
A |
T |
1: 75,232,356 (GRCm39) |
L453M |
probably damaging |
Het |
| Ptprz1 |
T |
A |
6: 23,000,569 (GRCm39) |
D886E |
probably damaging |
Het |
| Rcn1 |
T |
A |
2: 105,225,126 (GRCm39) |
I110F |
possibly damaging |
Het |
| Scn1a |
T |
A |
2: 66,154,977 (GRCm39) |
T661S |
probably benign |
Het |
| Slc6a19 |
A |
G |
13: 73,832,176 (GRCm39) |
Y467H |
possibly damaging |
Het |
| Slc9c1 |
T |
A |
16: 45,395,783 (GRCm39) |
D611E |
probably benign |
Het |
| Slitrk6 |
T |
C |
14: 110,989,395 (GRCm39) |
E104G |
possibly damaging |
Het |
| Spag17 |
A |
T |
3: 99,958,103 (GRCm39) |
K920N |
possibly damaging |
Het |
| St3gal5 |
A |
G |
6: 72,119,133 (GRCm39) |
S82G |
probably benign |
Het |
| Tlk1 |
T |
C |
2: 70,544,333 (GRCm39) |
*767W |
probably null |
Het |
| Tln2 |
A |
G |
9: 67,277,988 (GRCm39) |
V342A |
probably damaging |
Het |
| Tmem104 |
T |
A |
11: 115,093,006 (GRCm39) |
M132K |
probably damaging |
Het |
| Tmem184c |
A |
G |
8: 78,323,702 (GRCm39) |
S387P |
possibly damaging |
Het |
| Tmtc1 |
A |
G |
6: 148,327,411 (GRCm39) |
V34A |
possibly damaging |
Het |
| Trim46 |
A |
G |
3: 89,143,640 (GRCm39) |
F596S |
probably damaging |
Het |
| Unc79 |
T |
A |
12: 103,100,784 (GRCm39) |
D1870E |
possibly damaging |
Het |
| Utp20 |
T |
C |
10: 88,614,253 (GRCm39) |
T1234A |
probably benign |
Het |
| Vmn1r31 |
T |
A |
6: 58,449,728 (GRCm39) |
T46S |
probably benign |
Het |
| Vps13a |
A |
T |
19: 16,669,188 (GRCm39) |
L1341Q |
probably benign |
Het |
| Wdr72 |
A |
T |
9: 74,117,715 (GRCm39) |
D821V |
probably damaging |
Het |
| Zfhx4 |
T |
C |
3: 5,464,042 (GRCm39) |
L1400P |
probably damaging |
Het |
| Zfp217 |
T |
A |
2: 169,956,794 (GRCm39) |
K735* |
probably null |
Het |
| Zfp235 |
A |
G |
7: 23,836,541 (GRCm39) |
Q29R |
probably damaging |
Het |
| Zfp628 |
A |
G |
7: 4,923,167 (GRCm39) |
Y463C |
probably damaging |
Het |
| Zkscan4 |
A |
G |
13: 21,668,751 (GRCm39) |
T401A |
possibly damaging |
Het |
|
| Other mutations in Mthfd1l |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00932:Mthfd1l
|
APN |
10 |
3,989,971 (GRCm38) |
synonymous |
probably benign |
|
|
IGL01013:Mthfd1l
|
APN |
10 |
3,980,716 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01018:Mthfd1l
|
APN |
10 |
3,982,345 (GRCm39) |
splice site |
probably benign |
|
|
IGL01018:Mthfd1l
|
APN |
10 |
3,928,708 (GRCm39) |
missense |
probably benign |
|
|
IGL01018:Mthfd1l
|
APN |
10 |
3,957,800 (GRCm39) |
missense |
probably benign |
|
|
IGL01068:Mthfd1l
|
APN |
10 |
3,978,428 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01584:Mthfd1l
|
APN |
10 |
3,966,738 (GRCm39) |
missense |
probably damaging |
0.97 |
|
IGL01609:Mthfd1l
|
APN |
10 |
3,968,567 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL02272:Mthfd1l
|
APN |
10 |
3,991,812 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02344:Mthfd1l
|
APN |
10 |
3,998,272 (GRCm39) |
splice site |
probably null |
|
|
IGL02429:Mthfd1l
|
APN |
10 |
4,039,334 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02503:Mthfd1l
|
APN |
10 |
4,033,824 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02748:Mthfd1l
|
APN |
10 |
3,930,268 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL02748:Mthfd1l
|
APN |
10 |
3,968,587 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
IGL03031:Mthfd1l
|
APN |
10 |
3,968,601 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL03047:Mthfd1l
|
APN |
10 |
3,930,409 (GRCm39) |
splice site |
probably benign |
|
|
IGL03215:Mthfd1l
|
APN |
10 |
3,991,826 (GRCm39) |
missense |
probably benign |
0.14 |
|
IGL03367:Mthfd1l
|
APN |
10 |
4,056,536 (GRCm39) |
splice site |
probably benign |
|
|
R0047:Mthfd1l
|
UTSW |
10 |
3,928,727 (GRCm39) |
splice site |
probably benign |
|
|
R0047:Mthfd1l
|
UTSW |
10 |
3,928,727 (GRCm39) |
splice site |
probably benign |
|
|
R0348:Mthfd1l
|
UTSW |
10 |
4,006,766 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0496:Mthfd1l
|
UTSW |
10 |
4,040,006 (GRCm39) |
missense |
probably benign |
|
|
R0658:Mthfd1l
|
UTSW |
10 |
3,997,976 (GRCm39) |
splice site |
probably null |
|
|
R1177:Mthfd1l
|
UTSW |
10 |
3,935,661 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
R1676:Mthfd1l
|
UTSW |
10 |
4,033,877 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1703:Mthfd1l
|
UTSW |
10 |
4,098,093 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1888:Mthfd1l
|
UTSW |
10 |
4,056,528 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1888:Mthfd1l
|
UTSW |
10 |
4,056,528 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1891:Mthfd1l
|
UTSW |
10 |
3,982,284 (GRCm39) |
nonsense |
probably null |
|
|
R2014:Mthfd1l
|
UTSW |
10 |
3,997,894 (GRCm39) |
missense |
probably benign |
|
|
R2061:Mthfd1l
|
UTSW |
10 |
4,053,288 (GRCm39) |
missense |
probably benign |
0.00 |
|
R2197:Mthfd1l
|
UTSW |
10 |
3,978,399 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2360:Mthfd1l
|
UTSW |
10 |
4,006,771 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3085:Mthfd1l
|
UTSW |
10 |
4,040,007 (GRCm39) |
missense |
probably benign |
0.00 |
|
R3176:Mthfd1l
|
UTSW |
10 |
4,098,025 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3276:Mthfd1l
|
UTSW |
10 |
4,098,025 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4065:Mthfd1l
|
UTSW |
10 |
3,982,242 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4612:Mthfd1l
|
UTSW |
10 |
3,980,717 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4803:Mthfd1l
|
UTSW |
10 |
3,957,840 (GRCm39) |
missense |
possibly damaging |
0.52 |
|
R4883:Mthfd1l
|
UTSW |
10 |
3,957,775 (GRCm39) |
missense |
probably benign |
0.11 |
|
R4932:Mthfd1l
|
UTSW |
10 |
3,930,241 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5507:Mthfd1l
|
UTSW |
10 |
4,056,432 (GRCm39) |
missense |
probably benign |
0.20 |
|
R5687:Mthfd1l
|
UTSW |
10 |
3,940,002 (GRCm39) |
splice site |
probably null |
|
|
R5694:Mthfd1l
|
UTSW |
10 |
3,985,239 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
R5727:Mthfd1l
|
UTSW |
10 |
4,053,302 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R5908:Mthfd1l
|
UTSW |
10 |
4,039,392 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5951:Mthfd1l
|
UTSW |
10 |
3,998,222 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6330:Mthfd1l
|
UTSW |
10 |
3,930,234 (GRCm39) |
missense |
probably benign |
|
|
R6583:Mthfd1l
|
UTSW |
10 |
3,997,937 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R6846:Mthfd1l
|
UTSW |
10 |
3,997,898 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7105:Mthfd1l
|
UTSW |
10 |
4,053,261 (GRCm39) |
missense |
probably benign |
|
|
R7456:Mthfd1l
|
UTSW |
10 |
4,039,998 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7848:Mthfd1l
|
UTSW |
10 |
4,033,739 (GRCm39) |
missense |
possibly damaging |
0.81 |
|
R8003:Mthfd1l
|
UTSW |
10 |
3,934,147 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8073:Mthfd1l
|
UTSW |
10 |
3,923,417 (GRCm39) |
missense |
probably benign |
0.28 |
|
R8140:Mthfd1l
|
UTSW |
10 |
3,957,745 (GRCm39) |
nonsense |
probably null |
|
|
R8478:Mthfd1l
|
UTSW |
10 |
4,098,064 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8677:Mthfd1l
|
UTSW |
10 |
3,998,250 (GRCm39) |
missense |
possibly damaging |
0.58 |
|
R8943:Mthfd1l
|
UTSW |
10 |
3,978,466 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9086:Mthfd1l
|
UTSW |
10 |
3,923,412 (GRCm39) |
missense |
probably benign |
0.22 |
|
R9267:Mthfd1l
|
UTSW |
10 |
3,934,154 (GRCm39) |
missense |
probably benign |
|
|
R9371:Mthfd1l
|
UTSW |
10 |
4,053,335 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
X0003:Mthfd1l
|
UTSW |
10 |
4,039,303 (GRCm39) |
missense |
probably damaging |
0.99 |
|
Z1088:Mthfd1l
|
UTSW |
10 |
3,957,844 (GRCm39) |
missense |
probably benign |
0.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- GCCAGCAGTCACCATGTTAACCATC -3'
(R):5'- ACTCTCCCAAGTCCTAGCTCATCAG -3'
Sequencing Primer
(F):5'- TCCATAGCCGTACAACTGATAG -3'
(R):5'- GTCCTAGCTCATCAGAGCAG -3'
|
| Posted On |
2013-05-09 |
Incidental Mutation