Mutagenetix > Incidental Mutation

Incidental Mutation 'R9267:Mthfd1l'

702624

Institutional Source

Beutler Lab

Gene Symbol

Mthfd1l

Ensembl Gene

ENSMUSG00000040675

Gene Name

methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like

Synonyms

2410004L15Rik, Fthfsdc1

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9267 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

3923118-4117081 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 3934154 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 162 (D162G)

Ref Sequence

ENSEMBL: ENSMUSP00000036178 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000043735] [ENSMUST00000117291] [ENSMUST00000120585]

AlphaFold

Q3V3R1

Predicted Effect

probably benign
Transcript: ENSMUST00000043735
AA Change: D162G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000036178
Gene: ENSMUSG00000040675
AA Change: D162G

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: D162G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000112870
Gene: ENSMUSG00000040675
AA Change: D162G

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: D162G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000112897
Gene: ENSMUSG00000040675
AA Change: D162G

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: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.7%

Validation Efficiency

98% (79/81)

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc4	G	T	14: 118,869,657 (GRCm39)		probably benign	Het
Abcd2	T	A	15: 91,063,423 (GRCm39)	T422S	possibly damaging	Het
Acsl3	T	G	1: 78,674,623 (GRCm39)	I390S	probably damaging	Het
Adad1	T	A	3: 37,139,074 (GRCm39)		probably benign	Het
Adam3	A	G	8: 25,171,605 (GRCm39)	V742A	probably benign	Het
Adgra3	A	T	5: 50,155,618 (GRCm39)	I450K	possibly damaging	Het
Adgrb2	T	C	4: 129,885,901 (GRCm39)	S14P	possibly damaging	Het
Arfgef3	T	A	10: 18,475,028 (GRCm39)	I1553F	probably damaging	Het
Btbd16	C	T	7: 130,417,516 (GRCm39)	R344C	probably damaging	Het
Ccdc27	A	G	4: 154,117,441 (GRCm39)	L502P	probably damaging	Het
Ccdc50	T	A	16: 27,208,700 (GRCm39)	L5Q		Het
Cdh16	C	T	8: 105,341,834 (GRCm39)	G777D	probably damaging	Het
Cntn2	C	A	1: 132,449,021 (GRCm39)	V663L	probably benign	Het
Cpne4	T	A	9: 104,884,833 (GRCm39)	V343E	probably damaging	Het
Dctpp1	A	T	7: 126,856,275 (GRCm39)	I149N	probably benign	Het
Dlg5	T	C	14: 24,204,745 (GRCm39)	N1266S	probably damaging	Het
Dst	A	G	1: 34,232,145 (GRCm39)	D3246G	probably benign	Het
Efcab8	G	C	2: 153,646,861 (GRCm39)	V397L	unknown	Het
Erbin	T	C	13: 103,987,292 (GRCm39)	T423A	probably damaging	Het
Erich5	C	T	15: 34,471,563 (GRCm39)	P264L	possibly damaging	Het
Fam90a1a	A	G	8: 22,453,091 (GRCm39)	M149V	probably benign	Het
Fbxl18	C	T	5: 142,880,870 (GRCm39)	G62R	possibly damaging	Het
Fech	A	G	18: 64,591,267 (GRCm39)	S386P	possibly damaging	Het
Fhl3	T	A	4: 124,601,498 (GRCm39)		probably null	Het
Fkbp5	A	G	17: 28,629,558 (GRCm39)	S256P	probably benign	Het
Frem2	A	G	3: 53,564,504 (GRCm39)	M1T	probably null	Het
Galnt5	T	C	2: 57,925,220 (GRCm39)	F834L	possibly damaging	Het
Gm3618	G	T	14: 17,502,588 (GRCm39)	T99N	unknown	Het
Gm9195	T	A	14: 72,700,546 (GRCm39)	Q1127L	possibly damaging	Het
Gpsm1	A	G	2: 26,236,835 (GRCm39)	D643G	probably damaging	Het
Grm4	A	G	17: 27,654,183 (GRCm39)	V589A	possibly damaging	Het
Gskip	T	A	12: 105,665,052 (GRCm39)	F30L	probably benign	Het
Haus3	T	A	5: 34,311,452 (GRCm39)		probably null	Het
Heatr1	T	C	13: 12,421,489 (GRCm39)	F463S	probably damaging	Het
Hmcn1	G	A	1: 150,473,740 (GRCm39)	S4851F	probably benign	Het
Il16	A	C	7: 83,371,757 (GRCm39)	F16L	probably benign	Het
Itga1	C	A	13: 115,185,924 (GRCm39)	C26F	possibly damaging	Het
Itga6	A	G	2: 71,668,756 (GRCm39)	E565G	probably benign	Het
Itgb4	A	G	11: 115,870,465 (GRCm39)	H98R	probably benign	Het
Kidins220	T	A	12: 25,038,558 (GRCm39)	S37T	probably benign	Het
Lrrc37	A	T	11: 103,495,406 (GRCm39)	D2804E	unknown	Het
Lrrk2	C	T	15: 91,584,629 (GRCm39)	L349F	probably damaging	Het
Malrd1	T	G	2: 16,260,077 (GRCm39)	I2099S	unknown	Het
Mapk8ip1	A	G	2: 92,216,714 (GRCm39)	I492T	possibly damaging	Het
Mest	T	A	6: 30,742,141 (GRCm39)	D68E		Het
Nalcn	A	T	14: 123,518,567 (GRCm39)	D1657E	probably benign	Het
Nbeal2	C	A	9: 110,462,115 (GRCm39)	V1475F	probably damaging	Het
Nf1	C	A	11: 79,331,716 (GRCm39)	Q684K	possibly damaging	Het
Opn5	T	A	17: 42,903,793 (GRCm39)	T181S	probably damaging	Het
Or10ag54	T	C	2: 87,099,326 (GRCm39)	L67P	possibly damaging	Het
Or1j19	A	T	2: 36,676,530 (GRCm39)		probably benign	Het
Or7a38	A	G	10: 78,752,803 (GRCm39)	N43S	probably damaging	Het
Or9s15	A	T	1: 92,524,994 (GRCm39)	H251L	probably damaging	Het
Or9s15	A	T	1: 92,524,996 (GRCm39)	M252L	probably benign	Het
Orc4	T	A	2: 48,827,534 (GRCm39)	R20*	probably null	Het
Pik3ca	T	C	3: 32,492,211 (GRCm39)	Y270H	probably damaging	Het
Pkn2	T	C	3: 142,517,676 (GRCm39)	E474G	probably null	Het
Pnma8b	A	T	7: 16,679,159 (GRCm39)	N48Y	unknown	Het
Pnpla2	A	C	7: 141,036,503 (GRCm39)		probably benign	Het
Polr1a	G	A	6: 71,942,542 (GRCm39)	M1127I	probably benign	Het
Ptpre	A	C	7: 135,274,549 (GRCm39)	D507A	probably damaging	Het
Rab3gap2	T	C	1: 184,983,331 (GRCm39)	V490A	probably damaging	Het
Rab44	A	T	17: 29,354,338 (GRCm39)		probably benign	Het
Rchy1	G	T	5: 92,105,831 (GRCm39)	T39N	probably benign	Het
Ripor1	A	G	8: 106,348,063 (GRCm39)	D1146G	unknown	Het
Sh3yl1	A	T	12: 30,972,335 (GRCm39)	I35F	possibly damaging	Het
Slc22a5	A	G	11: 53,764,619 (GRCm39)	F276L	probably benign	Het
Slc8a3	T	A	12: 81,361,208 (GRCm39)	D537V	possibly damaging	Het
Smc4	T	A	3: 68,941,786 (GRCm39)	I1263N	probably damaging	Het
Snai2	A	T	16: 14,525,120 (GRCm39)	T209S	possibly damaging	Het
Stam2	A	T	2: 52,604,903 (GRCm39)	Y211N	probably damaging	Het
Stxbp1	A	G	2: 32,708,517 (GRCm39)	S83P	probably damaging	Het
Susd4	T	C	1: 182,716,389 (GRCm39)	F325L	probably benign	Het
Tmem245	A	G	4: 56,947,236 (GRCm39)	V59A	probably benign	Het
Tnk2	A	G	16: 32,494,489 (GRCm39)	D469G	probably damaging	Het
Tpx2	A	G	2: 152,732,517 (GRCm39)	D597G	probably damaging	Het
Ube2w	A	T	1: 16,612,011 (GRCm39)	S170R		Het
Vmn2r102	A	T	17: 19,896,928 (GRCm39)	I92F	probably damaging	Het
Vmn2r11	T	A	5: 109,199,929 (GRCm39)	E508V	possibly damaging	Het
Vmn2r30	T	A	7: 7,340,432 (GRCm39)	I21F	possibly damaging	Het
Yipf2	G	A	9: 21,501,489 (GRCm39)	T187M	possibly damaging	Het
Zbtb8a	T	A	4: 129,248,267 (GRCm39)	K335*	probably null	Het
Zfp609	T	C	9: 65,608,328 (GRCm39)	D1184G	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
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
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'- GTGTGCACATCTGTATGCAG -3'
(R):5'- CCAAGATACAGGACTTTCATTCAC -3'

Sequencing Primer
(F):5'- AACTCACTTTGCAGGCTAGG -3'
(R):5'- CGGAATTTTAAACATTCTCTACCTCC -3'

Posted On

2022-03-25