Mutagenetix > Incidental Mutation

Incidental Mutation 'PIT4377001:Gramd1a'

554922

Institutional Source

Beutler Lab

Gene Symbol

Gramd1a

Ensembl Gene

ENSMUSG00000001248

Gene Name

GRAM domain containing 1A

Synonyms

1300003M23Rik, D7Bwg0611e

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.137) question?

Stock #

PIT4377001 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

30829552-30855321 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 30843095 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 71 (I71N)

Ref Sequence

ENSEMBL: ENSMUSP00000001280 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000001280] [ENSMUST00000085636] [ENSMUST00000185514] [ENSMUST00000186634] [ENSMUST00000186723] [ENSMUST00000187679]

AlphaFold

Q8VEF1

Predicted Effect

possibly damaging
Transcript: ENSMUST00000001280
AA Change: I71N

PolyPhen 2 Score 0.947 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000001280
Gene: ENSMUSG00000001248
AA Change: I71N

Domain	Start	End	E-Value	Type
low complexity region	8	39	N/A	INTRINSIC
low complexity region	43	57	N/A	INTRINSIC
GRAM	93	160	2.54e-29	SMART
low complexity region	342	360	N/A	INTRINSIC
Pfam:DUF4782	372	520	7.3e-37	PFAM
low complexity region	531	542	N/A	INTRINSIC
low complexity region	548	562	N/A	INTRINSIC
transmembrane domain	606	628	N/A	INTRINSIC
low complexity region	707	719	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000085636
AA Change: I71N

PolyPhen 2 Score 0.864 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000082778
Gene: ENSMUSG00000001248
AA Change: I71N

Domain	Start	End	E-Value	Type
low complexity region	8	39	N/A	INTRINSIC
low complexity region	43	57	N/A	INTRINSIC
GRAM	93	160	2.54e-29	SMART
low complexity region	342	360	N/A	INTRINSIC
Pfam:DUF4782	372	500	1.1e-28	PFAM
low complexity region	514	528	N/A	INTRINSIC
transmembrane domain	572	594	N/A	INTRINSIC
low complexity region	673	685	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000185514
AA Change: I71N

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000139681
Gene: ENSMUSG00000001248
AA Change: I71N

Domain	Start	End	E-Value	Type
low complexity region	8	39	N/A	INTRINSIC
low complexity region	43	57	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000186634
AA Change: I71N

PolyPhen 2 Score 0.947 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000140195
Gene: ENSMUSG00000001248
AA Change: I71N

Domain	Start	End	E-Value	Type
low complexity region	8	39	N/A	INTRINSIC
low complexity region	43	57	N/A	INTRINSIC
GRAM	93	160	8.9e-32	SMART
low complexity region	342	360	N/A	INTRINSIC

Predicted Effect

SMART Domains

Protein: ENSMUSP00000139709
Gene: ENSMUSG00000001248
AA Change: I152N

Domain	Start	End	E-Value	Type
low complexity region	89	120	N/A	INTRINSIC
low complexity region	124	138	N/A	INTRINSIC
Pfam:GRAM	174	208	1e-6	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000187679
AA Change: I30N

PolyPhen 2 Score 0.947 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000140674
Gene: ENSMUSG00000001248
AA Change: I30N

Domain	Start	End	E-Value	Type
low complexity region	2	16	N/A	INTRINSIC
GRAM	52	119	8.9e-32	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000206432

Coding Region Coverage

1x: 92.9%
3x: 90.8%
10x: 85.9%
20x: 75.6%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700009N14Rik	T	C	4: 39,451,129 (GRCm39)	C112R	possibly damaging	Het
Acadl	G	A	1: 66,877,564 (GRCm39)	T329M	probably damaging	Het
Adgrv1	A	G	13: 81,677,104 (GRCm39)	L1909P	probably damaging	Het
Aff3	A	C	1: 38,578,044 (GRCm39)	V31G	probably damaging	Het
Bag3	A	G	7: 128,147,441 (GRCm39)	D352G	probably damaging	Het
Bcas3	A	T	11: 85,386,668 (GRCm39)	T368S	probably damaging	Het
Bmp3	A	G	5: 99,027,608 (GRCm39)	I434V	unknown	Het
Casq1	T	A	1: 172,039,568 (GRCm39)	T336S	probably benign	Het
Cib2	T	G	9: 54,467,271 (GRCm39)	E11A	probably damaging	Het
Cttn	C	A	7: 143,993,833 (GRCm39)	E393D	possibly damaging	Het
Dchs1	G	A	7: 105,406,795 (GRCm39)	R2237W	probably damaging	Het
Dclre1a	C	T	19: 56,532,837 (GRCm39)	A586T	probably benign	Het
Defb1	C	A	8: 22,266,716 (GRCm39)	Q17K	possibly damaging	Het
Dgat2	T	C	7: 98,806,342 (GRCm39)	Y285C	probably damaging	Het
Dhx57	A	T	17: 80,571,404 (GRCm39)	F732Y	probably damaging	Het
Dock2	T	G	11: 34,611,835 (GRCm39)	D176A	probably benign	Het
Epha6	A	G	16: 60,025,915 (GRCm39)	I509T	probably damaging	Het
Fblim1	C	T	4: 141,322,720 (GRCm39)	R21H	probably damaging	Het
Fbxw20	T	A	9: 109,050,795 (GRCm39)	H371L	probably benign	Het
Foxa1	T	A	12: 57,589,567 (GRCm39)	I218F	probably damaging	Het
Fstl1	A	T	16: 37,636,167 (GRCm39)	I53F	probably benign	Het
Gdnf	A	G	15: 7,864,011 (GRCm39)	R141G	probably benign	Het
Gemin7	G	A	7: 19,299,242 (GRCm39)	R118*	probably null	Het
Gm43218	T	C	6: 70,217,565 (GRCm39)	T64A	probably benign	Het
Gnat3	G	A	5: 18,220,557 (GRCm39)	M243I		Het
H4c12	C	G	13: 21,934,654 (GRCm39)	G8R	unknown	Het
Htt	A	T	5: 35,033,309 (GRCm39)	D1859V	probably benign	Het
Hyal1	T	C	9: 107,456,468 (GRCm39)	F415S	probably damaging	Het
Ighv1-47	T	C	12: 114,954,858 (GRCm39)	N74S	probably benign	Het
Igkv1-131	T	C	6: 67,743,192 (GRCm39)	R64G	probably benign	Het
Itgb1	T	A	8: 129,436,864 (GRCm39)	V95D	probably damaging	Het
Jak1	A	C	4: 101,036,748 (GRCm39)	N297K	probably benign	Het
Kcna4	T	A	2: 107,127,205 (GRCm39)	N646K	possibly damaging	Het
Krt42	A	G	11: 100,153,931 (GRCm39)	S442P	probably damaging	Het
Mcm3ap	G	A	10: 76,338,596 (GRCm39)	S1408N	possibly damaging	Het
Mdga2	T	A	12: 66,763,469 (GRCm39)	Q278L	probably damaging	Het
Mkln1	C	T	6: 31,451,289 (GRCm39)	T410M	probably damaging	Het
Nav3	T	C	10: 109,552,466 (GRCm39)	E1792G	probably damaging	Het
Ndrg1	A	G	15: 66,820,288 (GRCm39)	C49R	probably benign	Het
Neurl4	A	G	11: 69,801,232 (GRCm39)	H1201R	probably benign	Het
Nfasc	T	C	1: 132,510,804 (GRCm39)	Y1073C	unknown	Het
Nrbp2	A	G	15: 75,958,945 (GRCm39)	Y253H	probably benign	Het
Or10c1	T	A	17: 37,521,980 (GRCm39)	I255F	probably benign	Het
Or4g16	T	A	2: 111,137,225 (GRCm39)	V225D	probably damaging	Het
Or4k45	T	C	2: 111,395,556 (GRCm39)	T78A	probably damaging	Het
Pcsk5	A	T	19: 17,416,466 (GRCm39)	C1661S	probably damaging	Het
Qsox2	T	G	2: 26,110,924 (GRCm39)	D147A	probably damaging	Het
Siglec15	T	A	18: 78,100,590 (GRCm39)		probably benign	Het
Skint5	T	A	4: 113,454,900 (GRCm39)	T1011S	unknown	Het
Slc9a2	A	G	1: 40,783,001 (GRCm39)	T422A	probably damaging	Het
Tert	C	T	13: 73,776,380 (GRCm39)	T377I	possibly damaging	Het
Tex15	T	A	8: 34,061,129 (GRCm39)	S186R	probably damaging	Het
Tgfb1	A	G	7: 25,396,343 (GRCm39)	D212G	probably benign	Het
Tnc	T	G	4: 63,935,973 (GRCm39)	D321A	probably damaging	Het
Topbp1	G	A	9: 103,187,088 (GRCm39)	E98K	possibly damaging	Het
Ugp2	C	A	11: 21,320,203 (GRCm39)	M1I	probably null	Het
Vipr2	G	A	12: 116,058,418 (GRCm39)	D112N	probably benign	Het
Vps13a	T	C	19: 16,718,265 (GRCm39)	E485G	probably damaging	Het
Vps37a	T	A	8: 40,990,087 (GRCm39)	I198N	possibly damaging	Het
Zbtb9	T	C	17: 27,193,735 (GRCm39)	V380A	probably damaging	Het
Zfhx4	G	C	3: 5,307,802 (GRCm39)	V343L	probably damaging	Het

Other mutations in Gramd1a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01315:Gramd1a	APN	7	30,841,993 (GRCm39)	missense	probably damaging	0.99
IGL01627:Gramd1a	APN	7	30,839,221 (GRCm39)	missense	probably damaging	0.99
IGL01684:Gramd1a	APN	7	30,838,330 (GRCm39)	missense	possibly damaging	0.67
IGL01793:Gramd1a	APN	7	30,833,838 (GRCm39)	critical splice donor site	probably null
IGL01986:Gramd1a	APN	7	30,833,434 (GRCm39)	missense	possibly damaging	0.58
IGL02029:Gramd1a	APN	7	30,832,249 (GRCm39)	missense	possibly damaging	0.95
IGL02060:Gramd1a	APN	7	30,829,996 (GRCm39)	nonsense	probably null
IGL02569:Gramd1a	APN	7	30,829,932 (GRCm39)	unclassified	probably benign
IGL02606:Gramd1a	APN	7	30,833,940 (GRCm39)	missense	probably damaging	1.00
IGL02715:Gramd1a	APN	7	30,835,279 (GRCm39)	missense	probably damaging	1.00
IGL03253:Gramd1a	APN	7	30,839,271 (GRCm39)	nonsense	probably null
PIT4618001:Gramd1a	UTSW	7	30,832,021 (GRCm39)	missense	probably benign	0.00
R0179:Gramd1a	UTSW	7	30,841,843 (GRCm39)	missense	probably damaging	1.00
R0329:Gramd1a	UTSW	7	30,837,679 (GRCm39)	missense	possibly damaging	0.93
R0330:Gramd1a	UTSW	7	30,837,679 (GRCm39)	missense	possibly damaging	0.93
R0628:Gramd1a	UTSW	7	30,842,049 (GRCm39)	missense	probably damaging	1.00
R0834:Gramd1a	UTSW	7	30,837,589 (GRCm39)	missense	possibly damaging	0.94
R1421:Gramd1a	UTSW	7	30,842,291 (GRCm39)	missense	probably damaging	0.98
R1430:Gramd1a	UTSW	7	30,832,211 (GRCm39)	missense	probably damaging	0.97
R1682:Gramd1a	UTSW	7	30,842,325 (GRCm39)	splice site	probably null
R1703:Gramd1a	UTSW	7	30,838,959 (GRCm39)	missense	possibly damaging	0.96
R1822:Gramd1a	UTSW	7	30,841,998 (GRCm39)	missense	probably damaging	1.00
R2308:Gramd1a	UTSW	7	30,839,215 (GRCm39)	missense	probably damaging	0.97
R3861:Gramd1a	UTSW	7	30,835,365 (GRCm39)	missense	possibly damaging	0.90
R4184:Gramd1a	UTSW	7	30,831,940 (GRCm39)	intron	probably benign
R4908:Gramd1a	UTSW	7	30,838,292 (GRCm39)	missense	probably benign	0.27
R4978:Gramd1a	UTSW	7	30,832,213 (GRCm39)	missense	possibly damaging	0.74
R5723:Gramd1a	UTSW	7	30,833,908 (GRCm39)	missense	probably damaging	1.00
R5927:Gramd1a	UTSW	7	30,839,246 (GRCm39)	missense	probably benign	0.33
R6466:Gramd1a	UTSW	7	30,843,221 (GRCm39)	missense	probably benign
R6838:Gramd1a	UTSW	7	30,833,929 (GRCm39)	missense	probably benign	0.30
R7034:Gramd1a	UTSW	7	30,832,181 (GRCm39)	critical splice donor site	probably null
R7036:Gramd1a	UTSW	7	30,832,181 (GRCm39)	critical splice donor site	probably null
R7867:Gramd1a	UTSW	7	30,842,992 (GRCm39)	missense	probably damaging	1.00
R8729:Gramd1a	UTSW	7	30,843,248 (GRCm39)	missense	possibly damaging	0.53
R8783:Gramd1a	UTSW	7	30,832,220 (GRCm39)	missense	possibly damaging	0.50
R9147:Gramd1a	UTSW	7	30,837,606 (GRCm39)	unclassified	probably benign
R9485:Gramd1a	UTSW	7	30,829,963 (GRCm39)	missense	unknown
Z1186:Gramd1a	UTSW	7	30,843,198 (GRCm39)	missense	possibly damaging	0.93

Predicted Primers

PCR Primer
(F):5'- GCGTCTTATGTATCGCCCAC -3'
(R):5'- AGGCTAATTTCTGCCCCTAACC -3'

Sequencing Primer
(F):5'- AACTGCTCTCTCTGGTCTGGAG -3'
(R):5'- CACTCTGGCCGGAGCTC -3'

Posted On

2019-06-07