Mutagenetix > Incidental Mutation

Incidental Mutation 'R7211:Gpnmb'

561066

Institutional Source

Beutler Lab

Gene Symbol

Gpnmb

Ensembl Gene

ENSMUSG00000029816

Gene Name

glycoprotein (transmembrane) nmb

Synonyms

Osteoactivin, DC-HIL, Dchil

MMRRC Submission

045339-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7211 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

49013449-49044413 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 49028949 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 489 (I489T)

Ref Sequence

ENSEMBL: ENSMUSP00000031840 (fasta)

Gene Model

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

AlphaFold

Q99P91

Predicted Effect

possibly damaging
Transcript: ENSMUST00000031840
AA Change: I489T

PolyPhen 2 Score 0.819 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000031840
Gene: ENSMUSG00000029816
AA Change: I489T

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

possibly damaging
Transcript: ENSMUST00000204260
AA Change: I489T

PolyPhen 2 Score 0.819 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000145376
Gene: ENSMUSG00000029816
AA Change: I489T

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

Meta Mutation Damage Score

0.1712

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.6%

Validation Efficiency

99% (84/85)

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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
a	T	A	2: 154,887,699 (GRCm39)	V53E	probably damaging	Het
A1cf	A	G	19: 31,904,541 (GRCm39)	Y268C	probably benign	Het
Adam34l	T	A	8: 44,078,914 (GRCm39)	S437C	probably damaging	Het
Adamts13	C	T	2: 26,879,310 (GRCm39)	T621I	probably benign	Het
Akr1b7	A	T	6: 34,398,049 (GRCm39)	N293Y	probably benign	Het
Angpt2	T	A	8: 18,791,147 (GRCm39)	T50S	probably benign	Het
Anks1b	C	A	10: 90,346,932 (GRCm39)	A744D	possibly damaging	Het
Aqr	A	G	2: 113,965,204 (GRCm39)	V587A	probably benign	Het
Atm	A	G	9: 53,399,860 (GRCm39)	V1540A	probably benign	Het
Brd10	A	G	19: 29,763,712 (GRCm39)	F121S		Het
C4b	A	G	17: 34,954,508 (GRCm39)	V887A	possibly damaging	Het
Cd200r1	A	G	16: 44,609,120 (GRCm39)	T26A	probably benign	Het
Ciao1	A	G	2: 127,088,928 (GRCm39)		probably null	Het
Clba1	T	A	12: 112,774,632 (GRCm39)		probably null	Het
Clca3a2	A	G	3: 144,519,775 (GRCm39)	C200R	probably benign	Het
Col6a5	T	A	9: 105,805,363 (GRCm39)	Q1181L	unknown	Het
Copb2	T	A	9: 98,456,198 (GRCm39)	I244N	probably damaging	Het
Cpb2	A	G	14: 75,512,430 (GRCm39)	Y281C	probably damaging	Het
Disp3	C	A	4: 148,325,979 (GRCm39)	V1260F	probably damaging	Het
Dnajc2	C	T	5: 21,981,777 (GRCm39)	R123Q	probably damaging	Het
Dpysl2	T	C	14: 67,067,425 (GRCm39)	N162S	probably damaging	Het
Dsp	T	A	13: 38,372,511 (GRCm39)		probably null	Het
Edc4	T	A	8: 106,612,941 (GRCm39)		probably null	Het
Efcab3	C	A	11: 104,601,539 (GRCm39)	A284D	probably benign	Het
Efcab3	G	T	11: 104,615,435 (GRCm39)		probably null	Het
Epm2a	T	C	10: 11,219,419 (GRCm39)	Y69H	probably benign	Het
Frzb	C	A	2: 80,248,669 (GRCm39)	E262*	probably null	Het
Gaa	T	C	11: 119,175,030 (GRCm39)	V877A	possibly damaging	Het
Gpr31b	T	C	17: 13,271,104 (GRCm39)	T22A	probably benign	Het
Gys1	T	A	7: 45,097,684 (GRCm39)	F477Y	possibly damaging	Het
Hoxc11	A	C	15: 102,863,487 (GRCm39)	E176A	possibly damaging	Het
Kcnk13	T	A	12: 100,028,076 (GRCm39)	F384I	probably damaging	Het
Ky	A	G	9: 102,386,349 (GRCm39)	E59G	probably benign	Het
Lama4	T	A	10: 38,881,491 (GRCm39)	D93E	probably damaging	Het
Lrrc23	A	T	6: 124,755,152 (GRCm39)	N128K	probably benign	Het
Lrrc71	G	T	3: 87,650,633 (GRCm39)	Q210K	possibly damaging	Het
Map1a	G	A	2: 121,135,124 (GRCm39)	R1980H	probably benign	Het
Med15	T	C	16: 17,515,977 (GRCm39)	D15G	unknown	Het
Mfng	A	T	15: 78,657,268 (GRCm39)	S69T	probably benign	Het
Muc16	T	G	9: 18,409,866 (GRCm39)	S181R	probably damaging	Het
Mug1	A	T	6: 121,857,498 (GRCm39)	Q1074L	possibly damaging	Het
Myorg	A	G	4: 41,498,028 (GRCm39)	I534T	probably damaging	Het
Nbea	T	A	3: 55,912,322 (GRCm39)	N1155I	probably benign	Het
Nbeal1	T	G	1: 60,240,110 (GRCm39)	L159V	probably damaging	Het
Nudt1	C	A	5: 140,323,402 (GRCm39)	P118Q	possibly damaging	Het
Or2q1	A	T	6: 42,794,950 (GRCm39)	T182S	probably benign	Het
Or8g37	A	C	9: 39,731,154 (GRCm39)	Q73P	possibly damaging	Het
Pcdhga6	T	A	18: 37,842,173 (GRCm39)	V631D	probably benign	Het
Pcna	A	C	2: 132,091,792 (GRCm39)	V203G	probably damaging	Het
Pgf	G	T	12: 85,222,549 (GRCm39)	N33K	probably benign	Het
Pgm2	T	C	5: 64,263,193 (GRCm39)	L280P	probably damaging	Het
Plcg1	G	A	2: 160,573,794 (GRCm39)	A20T	probably benign	Het
Pou2af2	G	T	9: 51,201,733 (GRCm39)	Q108K	probably damaging	Het
Prdx5	G	T	19: 6,884,958 (GRCm39)	D126E	probably damaging	Het
Prkag2	T	C	5: 25,200,296 (GRCm39)	T20A	probably benign	Het
Prr14l	T	A	5: 32,987,431 (GRCm39)	Q688L	probably damaging	Het
Pxdn	T	G	12: 30,034,903 (GRCm39)	D253E	possibly damaging	Het
Rbm18	A	T	2: 36,012,905 (GRCm39)	C53*	probably null	Het
Rprm	A	T	2: 53,975,270 (GRCm39)	L16Q	probably benign	Het
Saysd1	A	G	14: 20,127,576 (GRCm39)	F116S	probably damaging	Het
Scg3	A	G	9: 75,589,366 (GRCm39)	S96P	probably benign	Het
Scgb1b3	C	T	7: 31,075,078 (GRCm39)	L16F	unknown	Het
Sh3tc2	A	G	18: 62,122,474 (GRCm39)	T412A	probably benign	Het
Skint6	T	C	4: 113,095,566 (GRCm39)	N31S	probably benign	Het
Slc22a2	T	C	17: 12,805,770 (GRCm39)		probably null	Het
Slc8a2	C	T	7: 15,874,538 (GRCm39)	T262I	possibly damaging	Het
Smarcc1	A	T	9: 109,979,082 (GRCm39)	K188N	probably damaging	Het
Taf6	T	C	5: 138,177,088 (GRCm39)	T660A	possibly damaging	Het
Tbx2	C	T	11: 85,725,540 (GRCm39)	R164C	probably damaging	Het
Tec	T	C	5: 72,939,355 (GRCm39)	D220G	probably null	Het
Tfec	A	T	6: 16,867,464 (GRCm39)	W59R	probably damaging	Het
Tmtc2	G	T	10: 105,409,587 (GRCm39)	S8R	probably benign	Het
Tmtc3	A	T	10: 100,283,467 (GRCm39)	M696K	probably benign	Het
Trpc3	A	T	3: 36,694,882 (GRCm39)	S691T	possibly damaging	Het
Ttf2	A	T	3: 100,866,623 (GRCm39)	M503K	probably benign	Het
Ttll7	A	G	3: 146,619,031 (GRCm39)	H312R	probably damaging	Het
Ttn	T	C	2: 76,598,032 (GRCm39)	Y19627C	probably damaging	Het
Ugt2b35	T	C	5: 87,149,177 (GRCm39)	S143P	probably benign	Het
Usp53	A	G	3: 122,751,299 (GRCm39)	S253P	probably damaging	Het
Utp18	A	G	11: 93,776,206 (GRCm39)	V93A	probably benign	Het
Utrn	T	C	10: 12,277,079 (GRCm39)	N3413D	possibly damaging	Het
Zhx1	T	C	15: 57,916,647 (GRCm39)	D533G	possibly damaging	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
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
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'- TGTACGATCATCTCCGACCC -3'
(R):5'- ACCTCATTCTCAGTGCTACAGC -3'

Sequencing Primer
(F):5'- GATCATCTCCGACCCCACCTG -3'
(R):5'- GTGAGTTACTGCATACCTAAGCC -3'

Posted On

2019-06-26