Mutagenetix > Incidental Mutation

Incidental Mutation 'R4613:Gramd1b'

350979

Institutional Source

Beutler Lab

Gene Symbol

Gramd1b

Ensembl Gene

ENSMUSG00000040111

Gene Name

GRAM domain containing 1B

Synonyms

A930008A22Rik

MMRRC Submission

041824-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.123) question?

Stock #

R4613 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

40293233-40531383 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 40307993 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Aspartic acid at position 508 (V508D)

Ref Sequence

ENSEMBL: ENSMUSP00000130050 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000045682] [ENSMUST00000118159] [ENSMUST00000119373] [ENSMUST00000121357] [ENSMUST00000165104] [ENSMUST00000211853] [ENSMUST00000216821]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000045682
AA Change: V508D

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

SMART Domains

Protein: ENSMUSP00000048126
Gene: ENSMUSG00000040111
AA Change: V508D

Domain	Start	End	E-Value	Type
low complexity region	31	49	N/A	INTRINSIC
low complexity region	104	117	N/A	INTRINSIC
low complexity region	123	141	N/A	INTRINSIC
low complexity region	203	226	N/A	INTRINSIC
GRAM	240	307	1.54e-28	SMART
low complexity region	375	385	N/A	INTRINSIC
Pfam:DUF4782	519	667	1.6e-38	PFAM
low complexity region	696	710	N/A	INTRINSIC
transmembrane domain	768	790	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000118159
AA Change: V324D

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000112417
Gene: ENSMUSG00000040111
AA Change: V324D

Domain	Start	End	E-Value	Type
low complexity region	19	42	N/A	INTRINSIC
GRAM	56	123	1.54e-28	SMART
low complexity region	191	201	N/A	INTRINSIC
low complexity region	512	526	N/A	INTRINSIC
transmembrane domain	584	606	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000119373
AA Change: V391D

SMART Domains

Protein: ENSMUSP00000112489
Gene: ENSMUSG00000040111
AA Change: V391D

Domain	Start	End	E-Value	Type
low complexity region	9	24	N/A	INTRINSIC
low complexity region	86	101	N/A	INTRINSIC
GRAM	126	193	1.54e-28	SMART
low complexity region	261	271	N/A	INTRINSIC
low complexity region	582	596	N/A	INTRINSIC
transmembrane domain	654	676	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000121357
AA Change: V360D

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000112564
Gene: ENSMUSG00000040111
AA Change: V360D

Domain	Start	End	E-Value	Type
low complexity region	2	13	N/A	INTRINSIC
low complexity region	55	78	N/A	INTRINSIC
GRAM	92	159	1.54e-28	SMART
low complexity region	227	237	N/A	INTRINSIC
low complexity region	548	562	N/A	INTRINSIC
transmembrane domain	620	642	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000137454
AA Change: V118D

SMART Domains

Protein: ENSMUSP00000116871
Gene: ENSMUSG00000040111
AA Change: V118D

Domain	Start	End	E-Value	Type
Pfam:DUF4782	130	278	2.3e-39	PFAM
low complexity region	307	321	N/A	INTRINSIC
transmembrane domain	379	401	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155265

Predicted Effect

probably damaging
Transcript: ENSMUST00000165104
AA Change: V508D

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

SMART Domains

Protein: ENSMUSP00000130050
Gene: ENSMUSG00000040111
AA Change: V508D

Domain	Start	End	E-Value	Type
low complexity region	31	49	N/A	INTRINSIC
low complexity region	104	117	N/A	INTRINSIC
low complexity region	123	141	N/A	INTRINSIC
low complexity region	203	226	N/A	INTRINSIC
GRAM	240	307	1.54e-28	SMART
low complexity region	375	385	N/A	INTRINSIC
low complexity region	696	710	N/A	INTRINSIC
transmembrane domain	768	790	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000211853
AA Change: V393D

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

Predicted Effect

probably damaging
Transcript: ENSMUST00000216821
AA Change: V364D

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

Coding Region Coverage

1x: 99.4%
3x: 98.7%
10x: 97.4%
20x: 95.5%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9830107B12Rik	A	T	17: 48,128,557	L130I	probably benign	Het
Abca9	A	G	11: 110,144,784	V670A	probably benign	Het
Adad1	A	G	3: 37,092,033	N517D	probably damaging	Het
Ankle2	T	C	5: 110,231,379	L48P	probably benign	Het
Aoc3	A	T	11: 101,337,659		probably benign	Het
Areg	A	G	5: 91,143,504	K102R	probably benign	Het
Bmp1	T	C	14: 70,508,523	T167A	probably damaging	Het
C4b	C	T	17: 34,734,551	G986D	probably benign	Het
Caml	G	T	13: 55,625,142	G200C	probably damaging	Het
Ccdc40	A	C	11: 119,231,532	R53S	probably benign	Het
Cdh22	T	A	2: 165,143,656	I337L	probably benign	Het
Col12a1	A	T	9: 79,647,601	V2065D	probably benign	Het
Copg2	A	G	6: 30,811,596	S591P	probably benign	Het
Cyp2d34	G	A	15: 82,616,325	P438S	probably damaging	Het
Dchs1	T	C	7: 105,772,724	D163G	probably damaging	Het
Depdc1b	T	C	13: 108,363,643	V230A	probably damaging	Het
Depdc5	T	A	5: 32,975,446	L1300H	probably damaging	Het
Dnah10	G	T	5: 124,762,869		probably null	Het
Dsc2	A	T	18: 20,041,819	D466E	probably damaging	Het
Dthd1	A	G	5: 62,827,068	D372G	probably damaging	Het
Eogt	G	T	6: 97,134,304	Q199K	probably benign	Het
Epha6	C	A	16: 59,666,597	R1029L	possibly damaging	Het
Eppin	C	A	2: 164,589,323	E128*	probably null	Het
Fam102b	A	T	3: 109,027,255	F23I	probably benign	Het
Fam160b1	C	A	19: 57,371,187	P53Q	probably damaging	Het
Fgf20	T	C	8: 40,286,611	R33G	probably benign	Het
Fgg	A	G	3: 83,010,090	N142S	probably damaging	Het
Gba	C	T	3: 89,208,644		probably null	Het
Gli2	A	G	1: 118,837,511	V970A	probably damaging	Het
Gucy2c	T	A	6: 136,708,321	D898V	probably damaging	Het
Kcnj15	T	C	16: 95,295,794	Y92H	probably damaging	Het
L3mbtl3	A	T	10: 26,282,795	S652T	unknown	Het
Ldb2	G	T	5: 44,476,551	Q326K	probably benign	Het
Lipi	C	A	16: 75,560,801	R292L	probably benign	Het
Lrrc36	G	A	8: 105,449,614	V207I	possibly damaging	Het
Lyplal1	C	T	1: 186,088,752	G166D	probably benign	Het
Map1b	A	T	13: 99,430,302	Y1970*	probably null	Het
Map2	A	G	1: 66,425,469	N287D	probably damaging	Het
Map3k11	A	T	19: 5,697,470	Q578L	probably benign	Het
Map3k11	G	T	19: 5,697,471	Q578H	probably damaging	Het
Map4k4	G	A	1: 40,017,191	S1012N	probably benign	Het
Mapk13	A	T	17: 28,769,452	N15Y	probably damaging	Het
Mapk15	G	A	15: 75,995,910	A125T	probably damaging	Het
Mrgprb1	C	A	7: 48,447,708	R152L	possibly damaging	Het
Muc5ac	T	G	7: 141,791,103	Y104D	possibly damaging	Het
Myo1h	A	G	5: 114,348,379	N566S	possibly damaging	Het
Myo1h	C	A	5: 114,351,676	H647Q	probably benign	Het
Neo1	A	G	9: 58,889,041	I1201T	possibly damaging	Het
Nlgn1	T	C	3: 25,436,022	T514A	probably benign	Het
Olfr120	A	G	17: 37,726,696	Y224C	probably damaging	Het
Olfr533	A	T	7: 140,467,068	Y289F	probably damaging	Het
Olfr8	A	G	10: 78,956,065	N287D	probably damaging	Het
Olfr985	T	A	9: 40,127,722	K80*	probably null	Het
Orc2	A	T	1: 58,500,309	L57*	probably null	Het
Otoa	G	A	7: 121,145,568	V850M	probably damaging	Het
Pcnx3	T	C	19: 5,667,219	T1579A	possibly damaging	Het
Pde5a	A	T	3: 122,823,093	Y564F	probably damaging	Het
Pdxk	A	C	10: 78,447,919	I147S	probably damaging	Het
Pfdn5	A	G	15: 102,328,752	D108G	probably benign	Het
Pink1	T	C	4: 138,317,310	D342G	probably damaging	Het
Prkacb	A	T	3: 146,737,998	V336E	probably damaging	Het
Ptpro	C	A	6: 137,416,836	S13*	probably null	Het
Rfng	A	G	11: 120,782,650	L215P	probably damaging	Het
Rpn2	T	C	2: 157,302,425	F336L	possibly damaging	Het
Sacs	A	G	14: 61,211,797		probably null	Het
Sirpb1a	T	A	3: 15,417,037	Y77F	probably benign	Het
Skiv2l2	C	A	13: 112,921,739	E53*	probably null	Het
Slc30a8	A	G	15: 52,333,575	D294G	probably benign	Het
Sox13	T	C	1: 133,388,934	I212V	probably benign	Het
Srebf2	T	A	15: 82,185,348	I657N	possibly damaging	Het
Srsf6	C	A	2: 162,933,709	T146K	probably benign	Het
Strn4	T	C	7: 16,824,163	V162A	possibly damaging	Het
Sulf2	T	C	2: 166,132,605	D53G	probably damaging	Het
Tbc1d8	T	A	1: 39,372,708	I1016F	probably damaging	Het
Tfrc	G	T	16: 32,618,657	A278S	probably damaging	Het
Tnrc6a	T	G	7: 123,184,289		probably null	Het
Vmn1r83	T	C	7: 12,321,768	I121V	probably benign	Het
Vps13d	T	C	4: 145,131,655	S2200G	possibly damaging	Het
Washc2	T	A	6: 116,229,269	D397E	probably damaging	Het
Wipf3	T	C	6: 54,485,555	L250P	probably damaging	Het
Xirp1	A	G	9: 120,019,682	F45S	probably damaging	Het
Xpo5	A	G	17: 46,236,963	T910A	probably benign	Het
Zfp235	T	C	7: 24,141,676	Y507H	probably damaging	Het

Other mutations in Gramd1b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00490:Gramd1b	APN	9	40310041	missense	probably damaging	0.97
IGL00575:Gramd1b	APN	9	40327411	splice site	probably benign
IGL01596:Gramd1b	APN	9	40303513	missense	probably damaging	1.00
IGL01810:Gramd1b	APN	9	40315773	missense	probably damaging	1.00
IGL02148:Gramd1b	APN	9	40315764	missense	probably damaging	1.00
IGL02206:Gramd1b	APN	9	40300032	missense	probably benign	0.01
IGL02626:Gramd1b	APN	9	40298010	missense	probably damaging	0.98
IGL02723:Gramd1b	APN	9	40306831	missense	probably damaging	0.97
IGL03192:Gramd1b	APN	9	40306801	missense	probably damaging	1.00
I2288:Gramd1b	UTSW	9	40306805	missense	probably damaging	0.97
PIT4283001:Gramd1b	UTSW	9	40455456	missense	probably benign	0.01
R0038:Gramd1b	UTSW	9	40317526	missense	probably damaging	1.00
R0038:Gramd1b	UTSW	9	40317526	missense	probably damaging	1.00
R0600:Gramd1b	UTSW	9	40308355	missense	probably damaging	1.00
R1290:Gramd1b	UTSW	9	40316821	splice site	probably null
R1637:Gramd1b	UTSW	9	40304538	splice site	probably null
R1782:Gramd1b	UTSW	9	40413337	missense	probably damaging	1.00
R1928:Gramd1b	UTSW	9	40306469	missense	possibly damaging	0.70
R3620:Gramd1b	UTSW	9	40455546	missense	probably benign	0.01
R3943:Gramd1b	UTSW	9	40531044	start codon destroyed	probably null
R4740:Gramd1b	UTSW	9	40315832	splice site	probably null
R4808:Gramd1b	UTSW	9	40304349	missense	possibly damaging	0.58
R5407:Gramd1b	UTSW	9	40455655	missense	probably damaging	0.97
R6209:Gramd1b	UTSW	9	40333650	missense	probably damaging	1.00
R6797:Gramd1b	UTSW	9	40308406	missense	probably benign	0.34
R7103:Gramd1b	UTSW	9	40401606	missense	unknown
R7185:Gramd1b	UTSW	9	40333563	missense	probably benign	0.03
R7352:Gramd1b	UTSW	9	40307993	missense	probably damaging	1.00
R7409:Gramd1b	UTSW	9	40327431	missense	probably damaging	1.00
R7561:Gramd1b	UTSW	9	40401615	missense	unknown
R8272:Gramd1b	UTSW	9	40304524	missense	probably benign	0.00
R8474:Gramd1b	UTSW	9	40375911	critical splice donor site	probably null
R8690:Gramd1b	UTSW	9	40304378	missense	probably damaging	1.00
R8818:Gramd1b	UTSW	9	40304484	missense	probably benign	0.01
R9493:Gramd1b	UTSW	9	40306393	missense	probably damaging	1.00
R9648:Gramd1b	UTSW	9	40333497	missense	probably damaging	0.98

Predicted Primers

PCR Primer
(F):5'- TCAGGGAGAGATGAGCCTGC -3'
(R):5'- AATTCAGGTCTGGAGAACCCC -3'

Sequencing Primer
(F):5'- GATGAGCCTGCAGATCAGACC -3'
(R):5'- GTGTGTTCCCCATACCAAGCAG -3'

Posted On

2015-10-08