Mutagenetix > Incidental Mutation

Incidental Mutation 'R4697:Glmp'

355758

Institutional Source

Beutler Lab

Gene Symbol

Glmp

Ensembl Gene

ENSMUSG00000001418

Gene Name

glycosylated lysosomal membrane protein

Synonyms

NCU-G1, 0610031J06Rik

MMRRC Submission

041947-MU

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4697 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

88325023-88331313 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 88328274 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 47 (V47A)

Ref Sequence

ENSEMBL: ENSMUSP00000134809 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000001454] [ENSMUST00000001456] [ENSMUST00000107552] [ENSMUST00000107553] [ENSMUST00000131666] [ENSMUST00000154381] [ENSMUST00000176425] [ENSMUST00000176519] [ENSMUST00000177005] [ENSMUST00000193872]

AlphaFold

Q9JHJ3

Predicted Effect

probably damaging
Transcript: ENSMUST00000001454
AA Change: V308A

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000001454
Gene: ENSMUSG00000001418
AA Change: V308A

Domain	Start	End	E-Value	Type
signal peptide	1	35	N/A	INTRINSIC
Pfam:NCU-G1	53	130	2.7e-26	PFAM
Pfam:NCU-G1	124	333	4.8e-77	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000001456

SMART Domains

Protein: ENSMUSP00000001456
Gene: ENSMUSG00000001420

Domain	Start	End	E-Value	Type
low complexity region	30	43	N/A	INTRINSIC
low complexity region	79	89	N/A	INTRINSIC
low complexity region	177	192	N/A	INTRINSIC
transmembrane domain	197	219	N/A	INTRINSIC
transmembrane domain	234	256	N/A	INTRINSIC
transmembrane domain	280	302	N/A	INTRINSIC
transmembrane domain	312	330	N/A	INTRINSIC
transmembrane domain	337	359	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000107552

SMART Domains

Protein: ENSMUSP00000103176
Gene: ENSMUSG00000001420

Domain	Start	End	E-Value	Type
low complexity region	30	43	N/A	INTRINSIC
low complexity region	79	89	N/A	INTRINSIC
low complexity region	177	192	N/A	INTRINSIC
transmembrane domain	197	219	N/A	INTRINSIC
transmembrane domain	234	256	N/A	INTRINSIC
transmembrane domain	280	302	N/A	INTRINSIC
transmembrane domain	312	330	N/A	INTRINSIC
transmembrane domain	337	359	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000107553

SMART Domains

Protein: ENSMUSP00000103177
Gene: ENSMUSG00000001420

Domain	Start	End	E-Value	Type
low complexity region	30	43	N/A	INTRINSIC
low complexity region	79	89	N/A	INTRINSIC
low complexity region	177	192	N/A	INTRINSIC
transmembrane domain	197	219	N/A	INTRINSIC
transmembrane domain	234	256	N/A	INTRINSIC
transmembrane domain	280	302	N/A	INTRINSIC
transmembrane domain	312	330	N/A	INTRINSIC
transmembrane domain	337	359	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000131666

SMART Domains

Protein: ENSMUSP00000120235
Gene: ENSMUSG00000001418

Domain	Start	End	E-Value	Type
signal peptide	1	35	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000140039

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152801

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153716

Predicted Effect

probably damaging
Transcript: ENSMUST00000154381
AA Change: V47A

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000134809
Gene: ENSMUSG00000001418
AA Change: V47A

Domain	Start	End	E-Value	Type
Pfam:NCU-G1	2	72	5.4e-18	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000176425
AA Change: V289A

PolyPhen 2 Score 0.090 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000135575
Gene: ENSMUSG00000001418
AA Change: V289A

Domain	Start	End	E-Value	Type
signal peptide	1	35	N/A	INTRINSIC
Pfam:NCU-G1	37	314	3.3e-94	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000176519

SMART Domains

Protein: ENSMUSP00000135263
Gene: ENSMUSG00000001418

Domain	Start	End	E-Value	Type
signal peptide	1	35	N/A	INTRINSIC
Pfam:NCU-G1	53	125	4.7e-26	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000177005
AA Change: V374A

PolyPhen 2 Score 0.090 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000135398
Gene: ENSMUSG00000001418
AA Change: V374A

Domain	Start	End	E-Value	Type
signal peptide	1	35	N/A	INTRINSIC
Pfam:NCU-G1	54	397	1.1e-104	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000193646

Predicted Effect

probably benign
Transcript: ENSMUST00000193872

SMART Domains

Protein: ENSMUSP00000141830
Gene: ENSMUSG00000001420

Domain	Start	End	E-Value	Type
low complexity region	30	43	N/A	INTRINSIC
low complexity region	79	89	N/A	INTRINSIC

Meta Mutation Damage Score

0.1506

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.0%
20x: 94.5%

Validation Efficiency

96% (75/78)

MGI Phenotype

PHENOTYPE: Homozygous mutants for this allele displayed spontaneous development of liver fibrosis at 6 months and various hepatic cell phenotypes. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9030624J02Rik	T	A	7: 118,791,448	I455N	probably damaging	Het
A2m	T	C	6: 121,638,284	M1T	probably null	Het
Aatf	T	A	11: 84,449,138	D449V	probably damaging	Het
Acbd3	T	A	1: 180,721,944		probably benign	Het
BC005561	A	G	5: 104,522,240	K1543E	probably benign	Het
Bicc1	T	A	10: 70,953,484	I366F	possibly damaging	Het
Ccdc74a	T	C	16: 17,649,749	S184P	possibly damaging	Het
Cntn4	T	C	6: 106,525,485	V401A	probably damaging	Het
Cux2	T	C	5: 121,873,753	T540A	probably damaging	Het
Disp2	G	T	2: 118,791,684	E966*	probably null	Het
Dpp7	A	G	2: 25,354,919	Y209H	probably benign	Het
Dstyk	T	A	1: 132,449,487	F277Y	probably damaging	Het
Dtx1	A	T	5: 120,694,408		probably null	Het
Ear-ps2	G	A	14: 44,047,060		noncoding transcript	Het
Ednra	T	C	8: 77,664,995	H422R	probably benign	Het
Erlec1	T	A	11: 30,952,640	I67F	probably benign	Het
Fam161b	G	A	12: 84,348,558		probably benign	Het
Gata5	A	T	2: 180,327,379	C345*	probably null	Het
Gm9762	T	A	3: 78,966,550		noncoding transcript	Het
Gnas	A	T	2: 174,298,080	D14V	probably damaging	Het
Gnl3	T	C	14: 31,017,329	S53G	probably damaging	Het
Grhl3	C	T	4: 135,548,466	V527M	probably damaging	Het
Hoxd10	T	A	2: 74,694,187	L281*	probably null	Het
Kif16b	T	G	2: 142,690,694	Y1175S	probably benign	Het
Kif2b	A	G	11: 91,576,846	S204P	probably benign	Het
Klhl40	T	A	9: 121,778,734	I320N	probably damaging	Het
Ksr2	G	A	5: 117,708,147	R693Q	probably damaging	Het
Mis12	A	G	11: 71,025,326	K62E	possibly damaging	Het
Mlc1	A	G	15: 88,974,777	C102R	probably damaging	Het
Muc5b	T	C	7: 141,857,361	I1348T	unknown	Het
Myh7b	A	G	2: 155,629,322	E1130G	probably damaging	Het
Nat8f4	T	C	6: 85,901,386	T52A	probably benign	Het
Nxpe2	C	A	9: 48,320,521	V379L	probably benign	Het
Olfr1231	C	A	2: 89,302,902	S230I	possibly damaging	Het
Olfr1231	T	A	2: 89,302,903	S230C	probably damaging	Het
Olfr1448	C	T	19: 12,919,934	C125Y	probably damaging	Het
Olfr1465	A	T	19: 13,313,717	D189E	probably benign	Het
Olfr288	G	A	15: 98,186,868	R310W	probably damaging	Het
Pcdhga7	A	T	18: 37,717,208	Y756F	probably damaging	Het
Pcsk6	T	A	7: 65,959,241	Y284N	probably damaging	Het
Pdcd11	T	C	19: 47,126,347	V1367A	possibly damaging	Het
Postn	T	A	3: 54,375,071	N484K	probably damaging	Het
Prkd3	C	T	17: 78,961,171	V572I	probably benign	Het
Qser1	T	C	2: 104,787,183	S1005G	probably benign	Het
Radil	G	T	5: 142,486,801	D951E	probably benign	Het
Ripk1	C	T	13: 34,027,942	R352*	probably null	Het
Sacs	T	C	14: 61,212,747	F4081L	probably benign	Het
Sbf1	A	G	15: 89,315,085	V11A	possibly damaging	Het
Sgip1	T	A	4: 102,934,587	F536I	probably damaging	Het
Slc45a1	A	G	4: 150,638,284	L381P	probably damaging	Het
Smarcad1	C	T	6: 65,052,641	P71L	probably benign	Het
Spns1	T	A	7: 126,377,037	D14V	probably damaging	Het
Sv2c	T	A	13: 95,986,018	I417F	possibly damaging	Het
Tas2r113	T	A	6: 132,893,516	M169K	probably benign	Het
Tgm1	A	T	14: 55,705,681	N567K	probably benign	Het
Tln2	C	T	9: 67,395,461	R76Q	probably damaging	Het
Trpm6	T	C	19: 18,853,791	V1340A	probably benign	Het
Tspan18	A	T	2: 93,312,030		probably null	Het
Txndc11	C	T	16: 11,084,314	V679I	probably damaging	Het
Usf1	G	T	1: 171,416,964	G144V	possibly damaging	Het
Vmn1r59	T	C	7: 5,454,452	Y103C	probably damaging	Het
Vmn2r23	A	T	6: 123,741,826	I713F	probably damaging	Het
Vmn2r79	A	T	7: 87,037,960	I850F	probably damaging	Het
Wdr90	C	T	17: 25,855,363	R676H	probably benign	Het
Zfp867	G	A	11: 59,463,661	R281W	probably damaging	Het
Zfp939	T	C	7: 39,472,942		noncoding transcript	Het

Other mutations in Glmp

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00484:Glmp	APN	3	88325862	splice site	probably null
IGL02551:Glmp	APN	3	88325082	start codon destroyed	probably null	0.53
IGL03212:Glmp	APN	3	88328357	missense	probably benign	0.01
R0325:Glmp	UTSW	3	88325084	start codon destroyed	probably null	0.72
R0719:Glmp	UTSW	3	88326145	nonsense	probably null
R0721:Glmp	UTSW	3	88326145	nonsense	probably null
R1617:Glmp	UTSW	3	88328119	splice site	probably benign
R1970:Glmp	UTSW	3	88327870	missense	probably damaging	1.00
R3824:Glmp	UTSW	3	88326411	missense	probably damaging	1.00
R3825:Glmp	UTSW	3	88326411	missense	probably damaging	1.00
R4521:Glmp	UTSW	3	88328039	missense	possibly damaging	0.60
R4806:Glmp	UTSW	3	88326013	intron	probably benign
R4823:Glmp	UTSW	3	88325223	intron	probably benign
R5035:Glmp	UTSW	3	88326644	splice site	probably benign
R5043:Glmp	UTSW	3	88326676	intron	probably benign
R5335:Glmp	UTSW	3	88326655	intron	probably benign
R5592:Glmp	UTSW	3	88326026	intron	probably benign
R5738:Glmp	UTSW	3	88326138	missense	probably benign	0.06
R5921:Glmp	UTSW	3	88325976	missense	probably benign	0.09
R6046:Glmp	UTSW	3	88325188	missense	probably damaging	0.96
R6103:Glmp	UTSW	3	88328031	missense	probably benign	0.02
R6859:Glmp	UTSW	3	88328042	missense	probably benign	0.30
R6943:Glmp	UTSW	3	88326610	missense	probably damaging	1.00
R6945:Glmp	UTSW	3	88325832	missense	probably benign	0.02
R7204:Glmp	UTSW	3	88326610	missense	probably damaging	1.00
R7770:Glmp	UTSW	3	88325770	missense	probably benign	0.39
R8022:Glmp	UTSW	3	88326520	missense	probably damaging	1.00
R8079:Glmp	UTSW	3	88325738	missense	probably damaging	0.98
R8296:Glmp	UTSW	3	88326273	missense	probably benign	0.16
R8986:Glmp	UTSW	3	88325695	missense	probably benign	0.28
R9266:Glmp	UTSW	3	88325729	missense	probably damaging	0.98
R9335:Glmp	UTSW	3	88328256	missense	probably damaging	0.98

Predicted Primers

PCR Primer
(F):5'- TTCAATCTGACCTTTGGGGC -3'
(R):5'- CTGAGGTTCTGCAGAAAAGC -3'

Sequencing Primer
(F):5'- GGGACCAATACTACCTTTGCTGG -3'
(R):5'- AAGCAGATCATGACCCTGGGC -3'

Posted On

2015-10-21