Mutagenetix > Incidental Mutation

Incidental Mutation 'R4932:Mthfd1l'

380655

Institutional Source

Beutler Lab

Gene Symbol

Mthfd1l

Ensembl Gene

ENSMUSG00000040675

Gene Name

methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like

Synonyms

2410004L15Rik, Fthfsdc1

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4932 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

3923118-4117081 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 3930241 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 112 (D112V)

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: D112V

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000036178
Gene: ENSMUSG00000040675
AA Change: D112V

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: D112V

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000112870
Gene: ENSMUSG00000040675
AA Change: D112V

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: D112V

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000112897
Gene: ENSMUSG00000040675
AA Change: D112V

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

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.5%
20x: 93.0%

Validation Efficiency

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: 84 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcf1	A	T	17: 36,270,342 (GRCm39)	V616E	possibly damaging	Het
Adam21	A	G	12: 81,605,692 (GRCm39)	V690A	probably benign	Het
Afg3l1	A	T	8: 124,228,119 (GRCm39)	T635S	probably damaging	Het
Ahcyl2	T	A	6: 29,890,700 (GRCm39)	M390K	probably benign	Het
Ank3	T	A	10: 69,734,053 (GRCm39)		probably null	Het
Antkmt	T	G	17: 26,010,652 (GRCm39)		probably null	Het
Arhgef3	A	T	14: 27,106,170 (GRCm39)	K151N	probably damaging	Het
Ccr3	T	G	9: 123,829,043 (GRCm39)	F126C	probably damaging	Het
Ccser1	A	G	6: 61,695,175 (GRCm39)	D170G	possibly damaging	Het
Celsr2	T	A	3: 108,310,074 (GRCm39)	D1552V	probably damaging	Het
Cfap69	G	A	5: 5,675,820 (GRCm39)	L265F	probably damaging	Het
Chrna9	C	T	5: 66,126,533 (GRCm39)	R92*	probably null	Het
Cog3	A	T	14: 75,970,394 (GRCm39)	V341D	probably damaging	Het
Csmd1	C	A	8: 16,073,779 (GRCm39)	R2072L	probably damaging	Het
Dbf4	G	T	5: 8,448,039 (GRCm39)	H390Q	probably benign	Het
Dcaf4	T	A	12: 83,579,078 (GRCm39)	C166S	possibly damaging	Het
Dclk3	T	A	9: 111,297,110 (GRCm39)	L218Q	possibly damaging	Het
Dip2b	T	A	15: 100,069,603 (GRCm39)	W643R	probably damaging	Het
Dip2c	A	G	13: 9,674,008 (GRCm39)	K1091E	probably damaging	Het
Dis3	T	A	14: 99,326,340 (GRCm39)	H415L	probably damaging	Het
Dnah7a	T	A	1: 53,542,737 (GRCm39)	I2478F	possibly damaging	Het
Dnah8	G	A	17: 30,967,542 (GRCm39)	D2585N	probably benign	Het
Doc2a	T	C	7: 126,447,752 (GRCm39)		probably benign	Het
Dph5	A	T	3: 115,693,456 (GRCm39)	M125L	probably benign	Het
Dst	A	T	1: 34,267,764 (GRCm39)	T5247S	possibly damaging	Het
Eno4	T	G	19: 58,952,889 (GRCm39)	V477G	possibly damaging	Het
Exosc8	T	C	3: 54,636,711 (GRCm39)	I207V	possibly damaging	Het
Fat4	T	A	3: 39,061,352 (GRCm39)	S4312T	probably benign	Het
Fgfr2	T	C	7: 129,843,007 (GRCm39)	D126G	probably damaging	Het
Fgfr4	A	G	13: 55,315,983 (GRCm39)	T799A	unknown	Het
Gcn1	A	T	5: 115,730,203 (GRCm39)	D839V	probably benign	Het
Gprin3	A	G	6: 59,331,158 (GRCm39)	V383A	probably benign	Het
Gpt	T	C	15: 76,583,040 (GRCm39)	V361A	probably benign	Het
Hepacam	G	A	9: 37,293,060 (GRCm39)	C217Y	probably damaging	Het
Hsp90aa1	A	T	12: 110,660,151 (GRCm39)	Y382N	probably damaging	Het
Htr2a	T	A	14: 74,879,462 (GRCm39)	N30K	probably benign	Het
Jhy	A	T	9: 40,872,299 (GRCm39)	M70K	possibly damaging	Het
Lrrc19	T	C	4: 94,529,174 (GRCm39)	Y36C	probably damaging	Het
Madcam1	C	T	10: 79,501,447 (GRCm39)	Q171*	probably null	Het
Mcm8	G	A	2: 132,680,629 (GRCm39)	M544I	probably benign	Het
Mdga1	C	T	17: 30,076,580 (GRCm39)	G64E	probably damaging	Het
Mmp3	A	G	9: 7,446,994 (GRCm39)	D58G	probably benign	Het
Ms4a10	T	C	19: 10,942,132 (GRCm39)	Y123C	probably damaging	Het
Ms4a4d	T	A	19: 11,535,296 (GRCm39)	I198K	probably benign	Het
N4bp2l2	A	C	5: 150,566,606 (GRCm39)	S567R	probably benign	Het
Ndufaf2	A	G	13: 108,295,010 (GRCm39)	Y32H	probably damaging	Het
Nup153	T	A	13: 46,866,213 (GRCm39)	K182*	probably null	Het
Or4c100	A	G	2: 88,356,079 (GRCm39)	T51A	probably benign	Het
Or52p2	A	G	7: 102,237,623 (GRCm39)	F109S	probably damaging	Het
Or5p4	T	A	7: 107,680,781 (GRCm39)	V260E	probably damaging	Het
Otoa	T	C	7: 120,754,358 (GRCm39)	S928P	probably damaging	Het
Oxct2a	T	C	4: 123,216,496 (GRCm39)	D295G	probably benign	Het
P4ha2	C	A	11: 54,015,846 (GRCm39)	T411K	probably benign	Het
Plcg2	A	T	8: 118,333,822 (GRCm39)	Q865L	probably benign	Het
Prepl	G	T	17: 85,385,932 (GRCm39)	T244K	possibly damaging	Het
Ptpro	A	T	6: 137,388,103 (GRCm39)	K776*	probably null	Het
Rc3h2	T	C	2: 37,279,844 (GRCm39)	K462E	possibly damaging	Het
Scn10a	A	G	9: 119,516,940 (GRCm39)		probably null	Het
Serpinb1c	A	G	13: 33,066,147 (GRCm39)	V266A	probably damaging	Het
Slc6a20b	T	A	9: 123,433,861 (GRCm39)	N326Y	probably damaging	Het
Spcs2	C	T	7: 99,508,038 (GRCm39)	G16D	possibly damaging	Het
Spns3	T	C	11: 72,390,321 (GRCm39)	D441G	possibly damaging	Het
Srsf4	A	G	4: 131,618,556 (GRCm39)	D49G	probably damaging	Het
Tec	A	T	5: 72,917,736 (GRCm39)	C494*	probably null	Het
Tecpr1	A	T	5: 144,141,476 (GRCm39)	Y798N	probably damaging	Het
Tex56	A	T	13: 35,116,613 (GRCm39)	T121S	possibly damaging	Het
Tmt1a	T	A	15: 100,202,987 (GRCm39)	F87Y	probably benign	Het
Trim56	C	T	5: 137,143,343 (GRCm39)	E58K	probably damaging	Het
Ttn	A	T	2: 76,626,478 (GRCm39)	D13146E	probably damaging	Het
Ube2q1	A	T	3: 89,686,790 (GRCm39)	K46*	probably null	Het
Ucn	G	T	5: 31,295,842 (GRCm39)	T8K	probably benign	Het
Usp25	T	C	16: 76,830,870 (GRCm39)		probably null	Het
Usp48	A	T	4: 137,343,144 (GRCm39)	Q430L	probably benign	Het
Usp48	A	T	4: 137,343,145 (GRCm39)		probably null	Het
Vill	A	T	9: 118,890,579 (GRCm39)	D164V	probably damaging	Het
Vmn2r91	T	A	17: 18,356,751 (GRCm39)	M806K	possibly damaging	Het
Wdfy4	T	A	14: 32,750,970 (GRCm39)	Y2256F	probably damaging	Het
Wsb1	A	G	11: 79,141,826 (GRCm39)	S64P	probably damaging	Het
Zc3h11a	C	A	1: 133,552,350 (GRCm39)	V586F	probably benign	Het
Zc3h12d	A	G	10: 7,729,014 (GRCm39)	D126G	probably damaging	Het
Zfp296	G	T	7: 19,313,637 (GRCm39)	C164F	possibly damaging	Het
Zfp442	T	A	2: 150,251,635 (GRCm39)	H89L	possibly damaging	Het
Zfp82	T	A	7: 29,756,312 (GRCm39)		probably null	Het
Zmynd8	A	G	2: 165,676,871 (GRCm39)	V249A	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
R0107:Mthfd1l	UTSW	10	3,991,838 (GRCm39)	missense	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
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'- CCCAGTTTCCATAGGCATTTAGAG -3'
(R):5'- AGATGCCCATAGTCCCGATG -3'

Sequencing Primer
(F):5'- CCATAGGCATTTAGAGTCTTTTCAG -3'
(R):5'- ATGAGCTAGGCTGACATTACCTC -3'

Posted On

2016-04-15