Mutagenetix > Incidental Mutation

Incidental Mutation 'R0242:Gpnmb'

59548

Institutional Source

Beutler Lab

Gene Symbol

Gpnmb

Ensembl Gene

ENSMUSG00000029816

Gene Name

glycoprotein (transmembrane) nmb

Synonyms

Osteoactivin, DC-HIL, Dchil

MMRRC Submission

038480-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0242 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

49013449-49044413 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 49024276 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 197 (N197S)

Ref Sequence

ENSEMBL: ENSMUSP00000145376 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000031840] [ENSMUST00000203757] [ENSMUST00000204260]

AlphaFold

Q99P91

Predicted Effect

probably damaging
Transcript: ENSMUST00000031840
AA Change: N197S

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000031840
Gene: ENSMUSG00000029816
AA Change: N197S

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
low complexity region	155	165	N/A	INTRINSIC
PKD	250	386	4.96e-9	SMART
transmembrane domain	500	522	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000203757

Predicted Effect

probably damaging
Transcript: ENSMUST00000204260
AA Change: N197S

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000145376
Gene: ENSMUSG00000029816
AA Change: N197S

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
low complexity region	155	165	N/A	INTRINSIC
PKD	250	386	4.96e-9	SMART
transmembrane domain	503	525	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000204460

Meta Mutation Damage Score

0.1422

Coding Region Coverage

1x: 99.4%
3x: 98.8%
10x: 97.3%
20x: 94.5%

Validation Efficiency

97% (110/113)

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 a type I transmembrane glycoprotein which shows homology to the pMEL17 precursor, a melanocyte-specific protein. GPNMB shows expression in the lowly metastatic human melanoma cell lines and xenografts but does not show expression in the highly metastatic cell lines. GPNMB may be involved in growth delay and reduction of metastatic potential. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutants exhibit dispersed pigmentation of the iris, deterioration of the posterior iris epithelium and slit-like transillumination defects. The mutation contributes to glaucoma, especially in combination with the brown coat color mutation. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 110 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700029H14Rik	T	C	8: 13,601,676 (GRCm39)	D230G	probably benign	Het
Abhd13	A	G	8: 10,037,561 (GRCm39)	I53V	probably benign	Het
Adgrl2	A	C	3: 148,544,821 (GRCm39)		probably null	Het
Aldh16a1	G	A	7: 44,794,088 (GRCm39)	A596V	probably damaging	Het
Aldh3b2	T	A	19: 4,029,414 (GRCm39)	Y262*	probably null	Het
Ambn	A	G	5: 88,615,831 (GRCm39)	Q420R	possibly damaging	Het
Ankib1	A	C	5: 3,750,344 (GRCm39)		probably benign	Het
Arhgap9	C	A	10: 127,165,407 (GRCm39)	H430Q	probably benign	Het
Arhgef25	C	T	10: 127,019,933 (GRCm39)	G435E	probably damaging	Het
Armc12	A	T	17: 28,751,366 (GRCm39)	D120V	possibly damaging	Het
Asxl3	G	A	18: 22,649,738 (GRCm39)	E576K	possibly damaging	Het
Bcdin3d	T	C	15: 99,368,776 (GRCm39)	E141G	probably benign	Het
Bmpr1b	G	A	3: 141,546,437 (GRCm39)	T483M	probably damaging	Het
Caprin2	C	T	6: 148,744,452 (GRCm39)	S991N	probably damaging	Het
Cd96	T	C	16: 45,892,129 (GRCm39)	I286M	possibly damaging	Het
Cdcp1	G	T	9: 123,009,237 (GRCm39)	F480L	probably benign	Het
Celf5	T	C	10: 81,300,243 (GRCm39)	T258A	probably benign	Het
Cgnl1	A	G	9: 71,628,939 (GRCm39)	V577A	probably damaging	Het
Clca3b	A	G	3: 144,547,226 (GRCm39)	S304P	probably benign	Het
Cmya5	A	T	13: 93,232,108 (GRCm39)	H993Q	probably benign	Het
Cnbp	A	T	6: 87,822,746 (GRCm39)	C6S	probably damaging	Het
Col14a1	C	T	15: 55,360,907 (GRCm39)	R1605W	probably damaging	Het
Cops7a	T	C	6: 124,941,817 (GRCm39)	N11S	probably benign	Het
Coro7	T	C	16: 4,448,042 (GRCm39)		probably benign	Het
Cpvl	T	C	6: 53,909,485 (GRCm39)	H217R	possibly damaging	Het
Cuedc1	T	C	11: 88,075,447 (GRCm39)		probably benign	Het
Cyp2c66	A	G	19: 39,130,369 (GRCm39)	Y68C	probably damaging	Het
Dicer1	G	A	12: 104,668,710 (GRCm39)	T1324M	probably benign	Het
Dlgap2	A	G	8: 14,777,562 (GRCm39)	D268G	probably benign	Het
Dnm1	T	A	2: 32,207,001 (GRCm39)	M535L	possibly damaging	Het
Dock7	A	T	4: 98,850,517 (GRCm39)	F1575Y	probably benign	Het
Dpp10	T	A	1: 123,326,275 (GRCm39)	H403L	possibly damaging	Het
Dync1h1	A	G	12: 110,616,285 (GRCm39)	D3112G	possibly damaging	Het
Eno3	A	G	11: 70,548,761 (GRCm39)	E21G	probably null	Het
Fam120b	T	A	17: 15,643,186 (GRCm39)	V655D	probably damaging	Het
Fkbp5	A	T	17: 28,647,426 (GRCm39)	D136E	probably benign	Het
Gdap1l1	T	A	2: 163,289,573 (GRCm39)	Y179*	probably null	Het
Gfer	A	G	17: 24,913,277 (GRCm39)	W192R	probably damaging	Het
Gm4782	A	G	6: 50,586,838 (GRCm39)	T408A	probably benign	Het
Golgb1	C	T	16: 36,695,992 (GRCm39)	Q164*	probably null	Het
Gtf2f1	G	A	17: 57,310,802 (GRCm39)	T414M	probably benign	Het
Hc	A	G	2: 34,926,166 (GRCm39)		probably benign	Het
Hcfc1	A	T	X: 72,992,035 (GRCm39)		probably benign	Het
Helz2	C	T	2: 180,872,223 (GRCm39)	R2539Q	probably damaging	Het
Hsd17b12	T	A	2: 93,988,160 (GRCm39)	I19F	probably benign	Het
Incenp	T	C	19: 9,871,114 (GRCm39)	T172A	unknown	Het
Jmy	A	G	13: 93,578,126 (GRCm39)	Y681H	probably benign	Het
Kbtbd11	A	G	8: 15,077,508 (GRCm39)	T36A	probably benign	Het
Kcnh4	T	C	11: 100,646,525 (GRCm39)	D267G	probably damaging	Het
Krt34	C	T	11: 99,932,157 (GRCm39)	E56K	probably damaging	Het
Krt40	T	A	11: 99,429,568 (GRCm39)	E335D	probably damaging	Het
Krt86	T	A	15: 101,374,454 (GRCm39)	Y282*	probably null	Het
Lgi3	C	T	14: 70,772,255 (GRCm39)	R267*	probably null	Het
Lnpk	A	G	2: 74,367,633 (GRCm39)		probably benign	Het
Lrp1b	T	A	2: 40,888,195 (GRCm39)	H2355L	probably benign	Het
Lrrc8e	G	A	8: 4,285,401 (GRCm39)	R542H	probably benign	Het
Mia2	T	C	12: 59,155,642 (GRCm39)	Y452H	probably damaging	Het
Mmachc	C	T	4: 116,561,738 (GRCm39)	R132Q	probably damaging	Het
Mtbp	T	A	15: 55,440,882 (GRCm39)	N356K	possibly damaging	Het
Myo5b	A	G	18: 74,794,787 (GRCm39)	H552R	possibly damaging	Het
Niban1	A	G	1: 151,593,967 (GRCm39)	D884G	probably benign	Het
Noxred1	A	G	12: 87,273,753 (GRCm39)	V96A	probably benign	Het
Nr1d2	T	A	14: 18,211,933 (GRCm38)	D390V	possibly damaging	Het
Oas1e	A	T	5: 120,929,839 (GRCm39)		probably benign	Het
Odad2	A	T	18: 7,211,516 (GRCm39)	V786D	probably damaging	Het
Or1r1	T	C	11: 73,874,538 (GRCm39)	S299G	probably benign	Het
Or6c1b	T	A	10: 129,273,217 (GRCm39)	Y179N	probably damaging	Het
Otog	G	T	7: 45,916,805 (GRCm39)	C914F	probably damaging	Het
Pank2	G	T	2: 131,122,117 (GRCm39)	C214F	probably damaging	Het
Pcdhb1	T	A	18: 37,399,788 (GRCm39)	S580T	probably benign	Het
Pdia3	T	C	2: 121,244,592 (GRCm39)	S2P	probably damaging	Het
Peli1	G	T	11: 21,092,602 (GRCm39)	R83L	probably damaging	Het
Pla2g3	T	A	11: 3,441,935 (GRCm39)	C366*	probably null	Het
Pon3	T	A	6: 5,240,860 (GRCm39)	D107V	probably benign	Het
Ppip5k2	A	G	1: 97,668,816 (GRCm39)	C532R	probably damaging	Het
Prph	A	T	15: 98,953,608 (GRCm39)	D174V	probably damaging	Het
Psd3	A	G	8: 68,210,738 (GRCm39)	M270T	probably damaging	Het
Pum3	A	G	19: 27,400,155 (GRCm39)		probably benign	Het
Pus1	A	T	5: 110,927,664 (GRCm39)	H30Q	probably benign	Het
Pwwp3a	T	C	10: 80,070,092 (GRCm39)	S354P	probably benign	Het
Rab7	A	T	6: 87,982,114 (GRCm39)	V87E	probably damaging	Het
Rbm5	A	T	9: 107,628,907 (GRCm39)		probably benign	Het
Reln	A	G	5: 22,147,595 (GRCm39)		probably null	Het
S1pr3	A	G	13: 51,572,938 (GRCm39)	T40A	probably benign	Het
Sdk1	T	A	5: 142,129,677 (GRCm39)		probably benign	Het
Senp7	T	A	16: 55,999,884 (GRCm39)	I853N	probably damaging	Het
Serpinb6c	T	A	13: 34,083,230 (GRCm39)		probably benign	Het
Shroom1	T	G	11: 53,356,312 (GRCm39)		probably null	Het
Slc24a3	T	C	2: 145,448,584 (GRCm39)	I376T	probably benign	Het
Slc46a1	T	C	11: 78,359,493 (GRCm39)	I375T	possibly damaging	Het
Slc4a9	T	C	18: 36,666,733 (GRCm39)	F527S	probably damaging	Het
Slc4a9	T	A	18: 36,674,286 (GRCm39)	I924N	probably damaging	Het
Slx4	T	A	16: 3,804,816 (GRCm39)	E666V	probably damaging	Het
Snrnp27	G	A	6: 86,652,575 (GRCm39)		probably benign	Het
Sorcs1	C	T	19: 50,216,659 (GRCm39)	G640E	probably damaging	Het
Spmap2l	G	T	5: 77,164,152 (GRCm39)	E52*	probably null	Het
Sptan1	A	T	2: 29,908,413 (GRCm39)	M1725L	probably benign	Het
Sync	G	A	4: 129,187,514 (GRCm39)	R182K	probably damaging	Het
Syne2	G	A	12: 76,144,808 (GRCm39)	G1586S	probably damaging	Het
Sytl1	G	T	4: 132,980,768 (GRCm39)	T522K	probably damaging	Het
Tex2	T	A	11: 106,410,781 (GRCm39)	K414*	probably null	Het
Tex55	C	T	16: 38,644,929 (GRCm39)		probably benign	Het
Thsd7a	G	A	6: 12,503,915 (GRCm39)	T413I	probably benign	Het
Tm9sf1	C	T	14: 55,875,392 (GRCm39)	A451T	possibly damaging	Het
Ttn	A	T	2: 76,656,496 (GRCm39)		probably benign	Het
Uba2	T	C	7: 33,854,054 (GRCm39)	I140V	possibly damaging	Het
Ushbp1	C	A	8: 71,842,762 (GRCm39)	G361*	probably null	Het
Wbp2nl	C	T	15: 82,197,988 (GRCm39)	A175V	probably benign	Het
Zc3h12d	A	G	10: 7,738,330 (GRCm39)	E212G	probably damaging	Het
Zc3h7b	T	C	15: 81,653,031 (GRCm39)		probably benign	Het

Other mutations in Gpnmb

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01064:Gpnmb	APN	6	49,032,593 (GRCm39)	missense	probably benign	0.01
IGL01291:Gpnmb	APN	6	49,032,615 (GRCm39)	missense	probably benign	0.12
IGL01307:Gpnmb	APN	6	49,022,299 (GRCm39)	missense	probably benign	0.03
IGL01398:Gpnmb	APN	6	49,027,365 (GRCm39)	missense	probably benign	0.02
IGL01531:Gpnmb	APN	6	49,024,392 (GRCm39)	splice site	probably benign
IGL01936:Gpnmb	APN	6	49,024,384 (GRCm39)	missense	probably null	1.00
ANU05:Gpnmb	UTSW	6	49,032,615 (GRCm39)	missense	probably benign	0.12
R0242:Gpnmb	UTSW	6	49,024,276 (GRCm39)	missense	probably damaging	0.99
R0413:Gpnmb	UTSW	6	49,019,737 (GRCm39)	missense	probably benign
R0690:Gpnmb	UTSW	6	49,024,949 (GRCm39)	missense	probably benign	0.24
R0884:Gpnmb	UTSW	6	49,024,847 (GRCm39)	missense	possibly damaging	0.65
R1659:Gpnmb	UTSW	6	49,024,786 (GRCm39)	missense	probably damaging	1.00
R3703:Gpnmb	UTSW	6	49,028,799 (GRCm39)	missense	possibly damaging	0.95
R3705:Gpnmb	UTSW	6	49,028,799 (GRCm39)	missense	possibly damaging	0.95
R4629:Gpnmb	UTSW	6	49,027,994 (GRCm39)	missense	possibly damaging	0.82
R4782:Gpnmb	UTSW	6	49,022,417 (GRCm39)	splice site	probably null
R4799:Gpnmb	UTSW	6	49,022,417 (GRCm39)	splice site	probably null
R4916:Gpnmb	UTSW	6	49,028,904 (GRCm39)	missense	probably damaging	1.00
R5223:Gpnmb	UTSW	6	49,033,139 (GRCm39)	missense	probably benign	0.01
R5390:Gpnmb	UTSW	6	49,024,775 (GRCm39)	missense	probably damaging	1.00
R5512:Gpnmb	UTSW	6	49,022,398 (GRCm39)	missense	possibly damaging	0.62
R5833:Gpnmb	UTSW	6	49,020,952 (GRCm39)	missense	probably damaging	1.00
R6103:Gpnmb	UTSW	6	49,019,820 (GRCm39)	missense	possibly damaging	0.86
R7211:Gpnmb	UTSW	6	49,028,949 (GRCm39)	missense	possibly damaging	0.82
R7900:Gpnmb	UTSW	6	49,027,400 (GRCm39)	missense	possibly damaging	0.83
R8859:Gpnmb	UTSW	6	49,028,964 (GRCm39)	splice site	probably benign
R9383:Gpnmb	UTSW	6	49,028,918 (GRCm39)	missense	probably damaging	1.00
R9393:Gpnmb	UTSW	6	49,024,996 (GRCm39)	missense	possibly damaging	0.89
Z1176:Gpnmb	UTSW	6	49,028,766 (GRCm39)	missense	possibly damaging	0.85

Predicted Primers

PCR Primer
(F):5'- AAGTTGCTTCATCGGGTTTTGCATC -3'
(R):5'- TAGGTAAGCCTTAGCGTCTCCCAG -3'

Sequencing Primer
(F):5'- CGCAGAGCAACCTTTAACCT -3'
(R):5'- AATAGCTAAGCTCTGCTGGAGTC -3'

Posted On

2013-07-11