Mutagenetix > Incidental Mutation

Incidental Mutation 'R2516:Gmds'

253837

Institutional Source

Beutler Lab

Gene Symbol

Gmds

Ensembl Gene

ENSMUSG00000038372

Gene Name

GDP-mannose 4, 6-dehydratase

Synonyms

MMRRC Submission

040420-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2516 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

32003562-32522723 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 32284456 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Isoleucine at position 219 (V219I)

Ref Sequence

ENSEMBL: ENSMUSP00000036696 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000041859]

AlphaFold

Q8K0C9

Predicted Effect

probably damaging
Transcript: ENSMUST00000041859
AA Change: V219I

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000036696
Gene: ENSMUSG00000038372
AA Change: V219I

Domain	Start	End	E-Value	Type
Pfam:RmlD_sub_bind	24	229	4.3e-8	PFAM
Pfam:Epimerase	26	274	2.2e-76	PFAM
Pfam:GDP_Man_Dehyd	27	358	7.2e-167	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000178294

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000222438

Meta Mutation Damage Score

0.5048

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.1%

Validation Efficiency

98% (65/66)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] GDP-mannose 4,6-dehydratase (GMD; EC 4.2.1.47) catalyzes the conversion of GDP-mannose to GDP-4-keto-6-deoxymannose, the first step in the synthesis of GDP-fucose from GDP-mannose, using NADP+ as a cofactor. The second and third steps of the pathway are catalyzed by a single enzyme, GDP-keto-6-deoxymannose 3,5-epimerase, 4-reductase, designated FX in humans (MIM 137020).[supplied by OMIM, Aug 2009]

Allele List at MGI

Other mutations in this stock

Total: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb11	A	T	2: 69,159,673 (GRCm39)	I6N	possibly damaging	Het
Aen	T	C	7: 78,555,616 (GRCm39)	V188A	probably damaging	Het
Afg3l1	A	G	8: 124,228,693 (GRCm39)	E753G	probably damaging	Het
Alas1	G	A	9: 106,115,859 (GRCm39)	T385I	probably damaging	Het
Alms1	C	A	6: 85,644,945 (GRCm39)		probably benign	Het
Ankrd65	A	G	4: 155,875,868 (GRCm39)	T30A	possibly damaging	Het
App	T	C	16: 84,775,117 (GRCm39)	S582G	probably damaging	Het
Arfgef1	A	T	1: 10,223,879 (GRCm39)	V1473E	possibly damaging	Het
Arhgap21	G	A	2: 20,859,809 (GRCm39)	P1196S	probably damaging	Het
Arhgap24	A	G	5: 103,039,776 (GRCm39)	T238A	probably benign	Het
Atf7	T	C	15: 102,437,439 (GRCm39)		probably benign	Het
Best1	G	T	19: 9,970,675 (GRCm39)	S55*	probably null	Het
Capn11	A	G	17: 45,944,725 (GRCm39)	V514A	probably damaging	Het
Cep104	T	A	4: 154,073,603 (GRCm39)	M52K	probably damaging	Het
Clca3a1	C	T	3: 144,443,619 (GRCm39)		probably null	Het
Cyp3a25	T	C	5: 145,939,837 (GRCm39)		probably null	Het
Dmxl2	G	A	9: 54,307,378 (GRCm39)	P2197S	probably damaging	Het
Drosha	T	C	15: 12,859,551 (GRCm39)		probably null	Het
Exosc9	A	G	3: 36,617,311 (GRCm39)	K355R	probably benign	Het
Fut1	A	C	7: 45,268,622 (GRCm39)	H192P	probably benign	Het
Gm572	T	A	4: 148,748,841 (GRCm39)	V166D	possibly damaging	Het
Gm9966	C	T	7: 95,607,735 (GRCm39)	P19S	unknown	Het
Gsn	G	A	2: 35,173,965 (GRCm39)	E25K	probably benign	Het
Il4i1	T	C	7: 44,489,315 (GRCm39)	F368S	probably damaging	Het
Irak1bp1	T	C	9: 82,712,373 (GRCm39)	L98P	probably damaging	Het
Khdrbs3	T	C	15: 68,896,544 (GRCm39)		probably benign	Het
Kndc1	T	C	7: 139,501,738 (GRCm39)	I925T	probably damaging	Het
Laptm4a	T	C	12: 8,988,151 (GRCm39)	I296T	probably benign	Het
Lpl	A	T	8: 69,340,170 (GRCm39)	H55L	probably benign	Het
Lrrk2	C	A	15: 91,640,130 (GRCm39)	N1558K	probably benign	Het
Mfsd2a	A	G	4: 122,844,280 (GRCm39)	L289P	probably damaging	Het
Mmrn2	T	A	14: 34,120,759 (GRCm39)	M543K	probably benign	Het
Mnat1	T	C	12: 73,228,550 (GRCm39)		probably benign	Het
Msto1	A	T	3: 88,819,200 (GRCm39)		probably null	Het
Mtus1	A	G	8: 41,535,776 (GRCm39)	Y647H	probably damaging	Het
Nars1	A	T	18: 64,638,087 (GRCm39)	V289E	probably damaging	Het
Oit3	T	A	10: 59,264,167 (GRCm39)	K322N	probably damaging	Het
Oit3	G	A	10: 59,277,507 (GRCm39)		probably benign	Het
Or4k1	T	C	14: 50,377,440 (GRCm39)	I219V	probably benign	Het
Or5b113	T	A	19: 13,342,557 (GRCm39)	C188*	probably null	Het
Or5m12	A	G	2: 85,734,900 (GRCm39)	I166T	probably benign	Het
Or6c211	G	A	10: 129,506,155 (GRCm39)	R78W	probably damaging	Het
Pecr	A	T	1: 72,316,469 (GRCm39)	C79S	probably damaging	Het
Plekhn1	T	C	4: 156,307,116 (GRCm39)	D478G	probably damaging	Het
Pls1	A	T	9: 95,658,616 (GRCm39)	M264K	probably benign	Het
Ptprj	C	A	2: 90,305,340 (GRCm39)		probably benign	Het
Pygm	A	G	19: 6,447,631 (GRCm39)	D646G	probably benign	Het
Rif1	GCCACCA	GCCA	2: 52,000,336 (GRCm39)		probably benign	Het
Scn8a	T	C	15: 100,867,043 (GRCm39)	V283A	probably benign	Het
Shisa5	T	C	9: 108,885,575 (GRCm39)		probably null	Het
Slc10a4	A	G	5: 73,165,848 (GRCm39)	I246V	possibly damaging	Het
Slc1a1	A	T	19: 28,870,312 (GRCm39)	I104F	probably benign	Het
Slc22a8	A	G	19: 8,587,559 (GRCm39)	Y511C	probably benign	Het
Slc6a5	A	G	7: 49,606,210 (GRCm39)	N706S	probably benign	Het
Sos2	T	C	12: 69,697,433 (GRCm39)	K96E	probably damaging	Het
Stom	G	A	2: 35,205,977 (GRCm39)	R251*	probably null	Het
Sycp1	T	C	3: 102,752,382 (GRCm39)	E800G	probably benign	Het
Tab2	G	A	10: 7,783,245 (GRCm39)	P679L	probably damaging	Het
Tiam2	G	A	17: 3,503,657 (GRCm39)	V945I	probably damaging	Het
Trpm5	G	T	7: 142,628,254 (GRCm39)	P1007Q	probably damaging	Het
Uchl1	T	G	5: 66,839,956 (GRCm39)	I139S	probably damaging	Het
Vmn1r232	A	G	17: 21,134,288 (GRCm39)	I104T	possibly damaging	Het
Vmn2r97	G	A	17: 19,167,814 (GRCm39)	M689I	probably benign	Het
Zc3h18	A	T	8: 123,129,904 (GRCm39)		probably benign	Het
Zfhx4	C	T	3: 5,468,418 (GRCm39)	P2859S	probably benign	Het
Zfp456	T	C	13: 67,510,491 (GRCm39)	K99R	probably benign	Het

Other mutations in Gmds

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00091:Gmds	APN	13	32,418,373 (GRCm39)	missense	probably damaging	1.00
IGL01021:Gmds	APN	13	32,311,013 (GRCm39)	missense	possibly damaging	0.85
IGL01463:Gmds	APN	13	32,418,341 (GRCm39)	missense	probably damaging	1.00
IGL01780:Gmds	APN	13	32,409,145 (GRCm39)	nonsense	probably null
IGL02570:Gmds	APN	13	32,418,390 (GRCm39)	splice site	probably benign
IGL02944:Gmds	APN	13	32,522,435 (GRCm39)	missense	probably benign
IGL03159:Gmds	APN	13	32,003,934 (GRCm39)	missense	probably damaging	1.00
Insipidus	UTSW	13	32,101,679 (GRCm39)	missense	probably benign	0.21
mini	UTSW	13	32,004,172 (GRCm39)	missense	possibly damaging	0.77
R0114:Gmds	UTSW	13	32,411,264 (GRCm39)	missense	probably benign	0.09
R0575:Gmds	UTSW	13	32,124,566 (GRCm39)	missense	probably damaging	1.00
R1932:Gmds	UTSW	13	32,311,980 (GRCm39)	missense	possibly damaging	0.87
R3877:Gmds	UTSW	13	32,411,248 (GRCm39)	missense	probably damaging	1.00
R4257:Gmds	UTSW	13	32,004,172 (GRCm39)	missense	possibly damaging	0.77
R4380:Gmds	UTSW	13	32,101,679 (GRCm39)	missense	probably benign	0.21
R4441:Gmds	UTSW	13	32,124,461 (GRCm39)	splice site	probably null
R5060:Gmds	UTSW	13	32,124,482 (GRCm39)	missense	probably benign	0.01
R5454:Gmds	UTSW	13	32,312,024 (GRCm39)	missense	probably damaging	1.00
R5493:Gmds	UTSW	13	32,124,488 (GRCm39)	missense	probably benign
R5571:Gmds	UTSW	13	32,101,704 (GRCm39)	splice site	probably null
R6795:Gmds	UTSW	13	32,418,335 (GRCm39)	critical splice donor site	probably null
R8463:Gmds	UTSW	13	32,003,906 (GRCm39)	missense	probably benign	0.01
R9138:Gmds	UTSW	13	32,311,035 (GRCm39)	nonsense	probably null
R9434:Gmds	UTSW	13	32,284,369 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CCATATTTGTGTCAGCAGAAGC -3'
(R):5'- AGAATTAGAGCTTCTTAACGTGTCC -3'

Sequencing Primer
(F):5'- GTGCCGGCCTCACATTTAAAG -3'
(R):5'- GAGCTTCTTAACGTGTCCAAATGAC -3'

Posted On

2014-12-04