Mutagenetix > Incidental Mutation

Incidental Mutation 'R1460:Dpm1'

162036

Institutional Source

Beutler Lab

Gene Symbol

Dpm1

Ensembl Gene

ENSMUSG00000078919

Gene Name

dolichyl-phosphate mannosyltransferase subunit 1, catalytic

Synonyms

MMRRC Submission

039515-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1460 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

168050968-168072299 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 168052549 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 229 (I229N)

Ref Sequence

ENSEMBL: ENSMUSP00000118776 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000057793] [ENSMUST00000088001] [ENSMUST00000109193] [ENSMUST00000138667] [ENSMUST00000154111]

AlphaFold

O70152

Predicted Effect

probably benign
Transcript: ENSMUST00000057793

SMART Domains

Protein: ENSMUSP00000056809
Gene: ENSMUSG00000051149

Domain	Start	End	E-Value	Type
ZnF_C2H2	74	97	6.57e0	SMART
ZnF_C2H2	107	129	1.77e1	SMART
low complexity region	130	141	N/A	INTRINSIC
ZnF_C2H2	165	188	1.29e1	SMART
ZnF_C2H2	221	244	1.4e1	SMART
low complexity region	423	437	N/A	INTRINSIC
ZnF_C2H2	446	468	8.62e1	SMART
ZnF_C2H2	488	509	2.54e1	SMART
ZnF_C2H2	511	534	1.03e-2	SMART
low complexity region	582	596	N/A	INTRINSIC
ZnF_C2H2	621	646	1.27e2	SMART
HOX	756	817	2.95e-6	SMART
low complexity region	957	970	N/A	INTRINSIC
low complexity region	1012	1023	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000088001

SMART Domains

Protein: ENSMUSP00000085316
Gene: ENSMUSG00000051149

Domain	Start	End	E-Value	Type
ZnF_C2H2	74	97	6.57e0	SMART
ZnF_C2H2	107	129	1.77e1	SMART
low complexity region	130	141	N/A	INTRINSIC
ZnF_C2H2	165	188	1.29e1	SMART
ZnF_C2H2	221	244	1.4e1	SMART
low complexity region	423	437	N/A	INTRINSIC
ZnF_C2H2	446	468	8.62e1	SMART
ZnF_C2H2	488	509	2.54e1	SMART
ZnF_C2H2	511	534	1.03e-2	SMART
low complexity region	582	596	N/A	INTRINSIC
ZnF_C2H2	621	646	1.27e2	SMART
HOX	756	817	2.95e-6	SMART
low complexity region	957	970	N/A	INTRINSIC
low complexity region	1012	1023	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000099072

SMART Domains

Protein: ENSMUSP00000096671
Gene: ENSMUSG00000078919

Domain	Start	End	E-Value	Type
Pfam:Glyco_tranf_2_3	16	118	1.8e-11	PFAM
Pfam:Glyco_tranf_2_2	20	119	1.3e-8	PFAM
Pfam:Glycos_transf_2	20	119	6.3e-28	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000109193
AA Change: I177N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000104816
Gene: ENSMUSG00000078919
AA Change: I177N

Domain	Start	End	E-Value	Type
Pfam:Glyco_tranf_2_2	2	101	1.2e-8	PFAM
Pfam:Glycos_transf_2	2	147	7.8e-36	PFAM
Pfam:Glyco_tranf_2_3	2	187	1.2e-11	PFAM
Pfam:Glyco_transf_21	34	148	1.1e-7	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131200

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000136582

Predicted Effect

probably damaging
Transcript: ENSMUST00000138667
AA Change: I229N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000139070
Gene: ENSMUSG00000093752
AA Change: I229N

Domain	Start	End	E-Value	Type
Pfam:Glyco_tranf_2_3	24	240	1.1e-13	PFAM
Pfam:Glyco_tranf_2_2	28	153	8.4e-10	PFAM
Pfam:Glycos_transf_2	28	199	3.8e-40	PFAM
Pfam:Glyco_transf_21	87	200	1.5e-7	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000154111
AA Change: I229N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000118776
Gene: ENSMUSG00000078919
AA Change: I229N

Domain	Start	End	E-Value	Type
Pfam:Glyco_tranf_2_3	24	241	3.2e-13	PFAM
Pfam:Glyco_tranf_2_2	28	153	7.6e-10	PFAM
Pfam:Glycos_transf_2	28	199	8.1e-41	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150437

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153258

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139984

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000140249

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141036

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 98.9%
3x: 98.0%
10x: 95.2%
20x: 89.1%

Validation Efficiency

94% (93/99)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Dolichol-phosphate mannose (Dol-P-Man) serves as a donor of mannosyl residues on the lumenal side of the endoplasmic reticulum (ER). Lack of Dol-P-Man results in defective surface expression of GPI-anchored proteins. Dol-P-Man is synthesized from GDP-mannose and dolichol-phosphate on the cytosolic side of the ER by the enzyme dolichyl-phosphate mannosyltransferase. Human DPM1 lacks a carboxy-terminal transmembrane domain and signal sequence and is regulated by DPM2. Mutations in this gene are associated with congenital disorder of glycosylation type Ie. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2015]

Allele List at MGI

Other mutations in this stock

Total: 96 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930522H14Rik	A	T	4: 109,388,407 (GRCm39)		probably null	Het
Abcb11	A	G	2: 69,087,718 (GRCm39)		probably benign	Het
Abi3bp	T	C	16: 56,382,780 (GRCm39)	V130A	probably damaging	Het
Adamts4	A	G	1: 171,084,009 (GRCm39)		probably benign	Het
Adgrd1	A	G	5: 129,199,627 (GRCm39)	T155A	possibly damaging	Het
Ano3	A	T	2: 110,513,103 (GRCm39)	S631T	probably damaging	Het
Ass1	G	A	2: 31,404,753 (GRCm39)	V345I	probably benign	Het
Atg7	G	A	6: 114,680,325 (GRCm39)	A384T	probably damaging	Het
Atp6v0a1	T	A	11: 100,924,824 (GRCm39)	I303N	probably damaging	Het
B3gntl1	T	G	11: 121,530,624 (GRCm39)	Y149S	probably damaging	Het
Btnl2	A	G	17: 34,585,424 (GRCm39)	D475G	probably benign	Het
Cdcp1	A	T	9: 123,009,092 (GRCm39)	S529T	possibly damaging	Het
Cenpt	A	G	8: 106,575,520 (GRCm39)	L194P	probably damaging	Het
Cfhr4	T	A	1: 139,625,934 (GRCm39)	I788F	probably damaging	Het
Chmp4b	A	G	2: 154,534,515 (GRCm39)	D177G	possibly damaging	Het
Chmp7	C	T	14: 69,956,899 (GRCm39)	M336I	probably benign	Het
Cish	G	T	9: 107,177,596 (GRCm39)	E91*	probably null	Het
Col22a1	T	C	15: 71,693,780 (GRCm39)	D740G	unknown	Het
Cplane2	T	C	4: 140,945,523 (GRCm39)	F125L	probably damaging	Het
Crocc	G	A	4: 140,756,551 (GRCm39)	Q1025*	probably null	Het
Ctrc	C	A	4: 141,566,120 (GRCm39)		probably benign	Het
Cyb5r2	T	A	7: 107,356,450 (GRCm39)	D7V	probably benign	Het
Dhx29	T	C	13: 113,101,744 (GRCm39)		probably benign	Het
Dhx9	A	C	1: 153,341,426 (GRCm39)	D607E	probably benign	Het
Dnajb7	C	T	15: 81,291,888 (GRCm39)	G150R	probably benign	Het
Dnase1l3	T	A	14: 7,974,050 (GRCm38)	T214S	probably benign	Het
Dstn	T	C	2: 143,780,408 (GRCm39)	V36A	possibly damaging	Het
Entpd1	T	C	19: 40,714,632 (GRCm39)	V247A	probably damaging	Het
Ephb3	C	A	16: 21,037,672 (GRCm39)	H277Q	probably benign	Het
Etl4	A	T	2: 20,793,288 (GRCm39)	N671I	probably damaging	Het
Fabp3	C	T	4: 130,206,180 (GRCm39)	T57I	probably benign	Het
Fancd2os	G	A	6: 113,574,973 (GRCm39)	T11I	probably damaging	Het
Fcrlb	G	T	1: 170,739,853 (GRCm39)		probably benign	Het
Fhip1a	T	C	3: 85,638,183 (GRCm39)	I39V	probably damaging	Het
Gm9991	T	C	1: 90,606,780 (GRCm39)		noncoding transcript	Het
Gstk1	C	T	6: 42,223,529 (GRCm39)	R40W	probably damaging	Het
Gstt1	C	T	10: 75,620,004 (GRCm39)	V190M	probably damaging	Het
Hectd2	G	A	19: 36,592,908 (GRCm39)	W691*	probably null	Het
Hecw2	T	C	1: 53,852,404 (GRCm39)	T1572A	probably damaging	Het
Hoxa5	T	C	6: 52,180,928 (GRCm39)	T135A	probably benign	Het
Igfl3	T	A	7: 17,913,880 (GRCm39)	C77S	possibly damaging	Het
Itgb4	A	G	11: 115,874,990 (GRCm39)	D449G	probably damaging	Het
Larp1b	T	C	3: 40,916,653 (GRCm39)	V11A	probably benign	Het
Lhx9	A	G	1: 138,766,447 (GRCm39)		probably benign	Het
Lig3	G	T	11: 82,686,624 (GRCm39)		probably benign	Het
Lipo4	A	C	19: 33,476,718 (GRCm39)	F343L	probably benign	Het
Lyn	T	A	4: 3,789,908 (GRCm39)	Y480*	probably null	Het
Mib2	C	T	4: 155,743,917 (GRCm39)	G42S	probably damaging	Het
Mill1	C	A	7: 17,996,595 (GRCm39)	A137D	probably damaging	Het
Mmut	T	C	17: 41,248,266 (GRCm39)	Y98H	probably damaging	Het
Morc2a	A	T	11: 3,633,794 (GRCm39)	R635S	probably benign	Het
Mpped2	A	G	2: 106,575,237 (GRCm39)		probably benign	Het
Mug2	T	C	6: 122,017,492 (GRCm39)		probably benign	Het
Mynn	C	A	3: 30,657,853 (GRCm39)	S57Y	probably damaging	Het
Myo3b	G	A	2: 70,062,798 (GRCm39)	E333K	probably benign	Het
Myt1	A	T	2: 181,444,725 (GRCm39)	I514F	probably damaging	Het
Nlrp4f	A	G	13: 65,338,082 (GRCm39)	C708R	probably benign	Het
Nod2	A	G	8: 89,390,440 (GRCm39)	E249G	probably damaging	Het
Npy2r	T	C	3: 82,448,251 (GRCm39)	I175V	probably benign	Het
Obscn	A	T	11: 58,946,792 (GRCm39)	V4114D	probably damaging	Het
Or1l8	A	T	2: 36,817,820 (GRCm39)	M102K	probably damaging	Het
Or2y12	T	A	11: 49,426,504 (GRCm39)	M164K	possibly damaging	Het
Or4a76	A	G	2: 89,460,282 (GRCm39)		probably null	Het
Or52e7	T	A	7: 104,684,915 (GRCm39)	I170N	possibly damaging	Het
Or8g33	A	G	9: 39,337,503 (GRCm39)	M288T	probably benign	Het
Pbxip1	T	A	3: 89,352,921 (GRCm39)	I196N	probably damaging	Het
Piezo1	G	A	8: 123,228,890 (GRCm39)	T209M	possibly damaging	Het
Polr1a	T	C	6: 71,918,368 (GRCm39)	M642T	probably damaging	Het
Prdm4	T	C	10: 85,743,686 (GRCm39)	M190V	probably benign	Het
Psmd7	G	A	8: 108,307,691 (GRCm39)	S264L	possibly damaging	Het
Qrich1	T	G	9: 108,410,846 (GRCm39)		probably benign	Het
Rapgef4	G	T	2: 71,861,520 (GRCm39)		probably null	Het
Rfx5	T	C	3: 94,863,636 (GRCm39)	I95T	probably damaging	Het
Rgr	G	A	14: 36,767,683 (GRCm39)	R113C	probably damaging	Het
Rnf20	T	C	4: 49,645,873 (GRCm39)		probably benign	Het
Rps3a1	G	A	3: 86,045,369 (GRCm39)	A241V	probably benign	Het
Rttn	A	T	18: 89,127,481 (GRCm39)		probably benign	Het
Scn2a	A	G	2: 65,532,187 (GRCm39)	T600A	probably damaging	Het
Scyl2	T	C	10: 89,493,751 (GRCm39)	D339G	possibly damaging	Het
Sipa1	T	A	19: 5,701,475 (GRCm39)	H1029L	probably benign	Het
Slc49a4	T	C	16: 35,539,736 (GRCm39)	T362A	probably benign	Het
Snrnp48	A	G	13: 38,395,081 (GRCm39)	T124A	probably benign	Het
Sptbn1	A	T	11: 30,088,637 (GRCm39)	M875K	possibly damaging	Het
Supt6	A	G	11: 78,113,024 (GRCm39)	V973A	possibly damaging	Het
Supv3l1	T	C	10: 62,279,162 (GRCm39)		probably benign	Het
Svep1	G	T	4: 58,068,740 (GRCm39)	N3015K	possibly damaging	Het
Tgfb3	A	G	12: 86,105,841 (GRCm39)		probably benign	Het
Trerf1	A	G	17: 47,628,771 (GRCm39)		noncoding transcript	Het
Trim24	T	A	6: 37,941,761 (GRCm39)	F904I	probably damaging	Het
Trim30d	T	A	7: 104,121,311 (GRCm39)	Y328F	probably benign	Het
Ttn	T	C	2: 76,698,717 (GRCm39)	E6G	probably damaging	Het
Ube2m	T	C	7: 12,769,762 (GRCm39)		probably benign	Het
Vmn2r-ps158	A	T	7: 42,672,639 (GRCm39)	R91S	probably benign	Het
Wdr90	A	T	17: 26,079,422 (GRCm39)	S237R	possibly damaging	Het
Zfp735	A	T	11: 73,603,159 (GRCm39)	H701L	possibly damaging	Het
Zp1	T	C	19: 10,896,242 (GRCm39)	D161G	probably benign	Het

Other mutations in Dpm1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00156:Dpm1	APN	2	168,052,495 (GRCm39)	missense	probably benign	0.37
PIT4531001:Dpm1	UTSW	2	168,052,472 (GRCm39)	missense	probably benign	0.42
R0200:Dpm1	UTSW	2	168,065,075 (GRCm39)	critical splice acceptor site	probably null
R0212:Dpm1	UTSW	2	168,069,414 (GRCm39)	missense	probably benign	0.00
R1889:Dpm1	UTSW	2	168,059,655 (GRCm39)	missense	possibly damaging	0.67
R1974:Dpm1	UTSW	2	168,059,667 (GRCm39)	missense	probably damaging	1.00
R4547:Dpm1	UTSW	2	168,065,073 (GRCm39)	missense	probably damaging	0.98
R4838:Dpm1	UTSW	2	168,052,456 (GRCm39)	missense	probably damaging	1.00
R4887:Dpm1	UTSW	2	168,059,679 (GRCm39)	missense	probably benign	0.01
R6919:Dpm1	UTSW	2	168,072,195 (GRCm39)	missense	probably damaging	1.00
R7169:Dpm1	UTSW	2	168,053,343 (GRCm39)	nonsense	probably null
R9526:Dpm1	UTSW	2	168,072,210 (GRCm39)	missense	probably benign
R9746:Dpm1	UTSW	2	168,072,307 (GRCm39)	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- ATGCAGGGAGCACTGCTTCATC -3'
(R):5'- TGTCGAGGACAGTGACCCTAAGAAC -3'

Sequencing Primer
(F):5'- CCTTTGGCTCATGTGTTAAGACAAC -3'
(R):5'- CCTAAGAACCGAGATTGTCAGTG -3'

Posted On

2014-03-14