Mutagenetix > Incidental Mutation

Incidental Mutation 'R9170:Large1'

696351

Institutional Source

Beutler Lab

Gene Symbol

Large1

Ensembl Gene

ENSMUSG00000004383

Gene Name

LARGE xylosyl- and glucuronyltransferase 1

Synonyms

froggy, enr, BPFD#36, fg

MMRRC Submission

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.612) question?

Stock #

R9170 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

73541227-74080164 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 73542645 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Phenylalanine at position 693 (Y693F)

Ref Sequence

ENSEMBL: ENSMUSP00000004497 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000004497] [ENSMUST00000119826] [ENSMUST00000212459]

AlphaFold

Q9Z1M7

Predicted Effect

probably benign
Transcript: ENSMUST00000004497
AA Change: Y693F

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000004497
Gene: ENSMUSG00000004383
AA Change: Y693F

Domain	Start	End	E-Value	Type
transmembrane domain	12	34	N/A	INTRINSIC
coiled coil region	55	90	N/A	INTRINSIC
Pfam:Glyco_transf_8	141	387	6.2e-22	PFAM
Pfam:Glyco_transf_49	473	540	5.2e-15	PFAM
Pfam:Glyco_transf_49	535	743	1.1e-47	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000119826
AA Change: Y693F

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000112617
Gene: ENSMUSG00000004383
AA Change: Y693F

Domain	Start	End	E-Value	Type
transmembrane domain	12	34	N/A	INTRINSIC
coiled coil region	55	90	N/A	INTRINSIC
Pfam:Glyco_transf_8	142	386	3e-23	PFAM
Pfam:Glyco_transf_49	473	540	2.3e-11	PFAM
Pfam:Glyco_transf_49	520	743	2.7e-44	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000212459
AA Change: Y693F

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.2%

Validation Efficiency

98% (61/62)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene, which is one of the largest in the human genome, encodes a member of the N-acetylglucosaminyltransferase gene family. It encodes a glycosyltransferase which participates in glycosylation of alpha-dystroglycan, and may carry out the synthesis of glycoprotein and glycosphingolipid sugar chains. It may also be involved in the addition of a repeated disaccharide unit. Mutations in this gene cause MDC1D, a novel form of congenital muscular dystrophy with severe mental retardation and abnormal glycosylation of alpha-dystroglycan. Alternative splicing of this gene results in two transcript variants that encode the same protein. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes exhibit a progressive myopathy, abnormal posture, thoracic kyphosis, calcium deposits in muscle, loss of Schwann cells and myelin, eye and CNS defects, deafness, reduced growth, and death around 4 months. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam4	T	C	12: 81,466,516 (GRCm39)	K702E	probably benign	Het
Agbl1	T	C	7: 75,985,069 (GRCm39)	I162T		Het
Agpat2	A	T	2: 26,487,230 (GRCm39)	I101N	possibly damaging	Het
Amot	A	T	X: 144,244,745 (GRCm39)	L435H		Het
Arhgap32	G	A	9: 32,162,039 (GRCm39)	R330H	possibly damaging	Het
Asb4	T	A	6: 5,390,775 (GRCm39)	I56N	probably benign	Het
Atp2a2	C	T	5: 122,604,087 (GRCm39)	V449M	possibly damaging	Het
Bend4	A	G	5: 67,575,080 (GRCm39)	L267P	probably damaging	Het
Catspere2	T	A	1: 177,967,949 (GRCm39)	N745K	probably benign	Het
Celf2	A	G	2: 6,554,646 (GRCm39)	F484L	possibly damaging	Het
Chd3	T	C	11: 69,241,648 (GRCm39)	D1495G	possibly damaging	Het
Chrna3	A	T	9: 54,933,671 (GRCm39)	V8D	unknown	Het
Cog3	T	C	14: 75,966,802 (GRCm39)	Y466C	probably damaging	Het
Col5a1	A	G	2: 27,841,363 (GRCm39)	E328G	unknown	Het
Col7a1	A	G	9: 108,785,707 (GRCm39)	Y392C	unknown	Het
Crtc3	A	T	7: 80,248,697 (GRCm39)	N255K	probably damaging	Het
Dnaaf1	T	C	8: 120,302,195 (GRCm39)	I32T	probably benign	Het
Dner	A	T	1: 84,512,647 (GRCm39)	C307S	probably damaging	Het
Dzip3	T	C	16: 48,772,401 (GRCm39)	K423E	possibly damaging	Het
Eif2b4	A	G	5: 31,345,393 (GRCm39)	S414P	probably damaging	Het
Elp4	T	C	2: 105,624,891 (GRCm39)	E334G	probably damaging	Het
Emilin2	T	A	17: 71,587,689 (GRCm39)	N141I	probably benign	Het
Fstl1	T	A	16: 37,647,140 (GRCm39)	V170E	probably damaging	Het
Fxn	A	G	19: 24,244,687 (GRCm39)	I151T	probably damaging	Het
Gtf3c4	A	T	2: 28,730,214 (GRCm39)	V9E	possibly damaging	Het
Ino80d	A	G	1: 63,132,607 (GRCm39)	S19P	probably damaging	Het
Kank3	T	G	17: 34,037,242 (GRCm39)	L370R	probably damaging	Het
Lig4	C	A	8: 10,022,202 (GRCm39)	W526L	probably damaging	Het
Mib1	C	T	18: 10,726,437 (GRCm39)	P45S	probably benign	Het
Ndufaf6	T	C	4: 11,070,301 (GRCm39)	K107E	probably benign	Het
Nf1	T	C	11: 79,436,291 (GRCm39)	L1977P	probably damaging	Het
Nme4	G	T	17: 26,314,389 (GRCm39)	A13E	probably benign	Het
Or52s6	G	A	7: 103,091,850 (GRCm39)	P160L	probably damaging	Het
Or52z15	T	A	7: 103,332,404 (GRCm39)	F160I	probably benign	Het
Pappa	G	A	4: 65,258,962 (GRCm39)	R1570Q	probably damaging	Het
Parp6	G	A	9: 59,531,213 (GRCm39)	A32T		Het
Pclo	A	G	5: 14,731,068 (GRCm39)	Q64R		Het
Pde8a	C	T	7: 80,982,619 (GRCm39)	T746I	probably damaging	Het
Perm1	TGCCTCTGAGCCTGACACGGCTTTGTCTACACCCGCCTCTGAGCCTGACACGGCTTTGTCTACACCCGCCTCTGAGCCTGACACGGCTTTGTCTACACCCGCCTCT	TGCCTCTGAGCCTGACACGGCTTTGTCTACACCCGCCTCTGAGCCTGACACGGCTTTGTCTACACCCGCCTCT	4: 156,302,525 (GRCm39)		probably benign	Het
Pramel21	T	C	4: 143,341,600 (GRCm39)	S10P	possibly damaging	Het
Prdm13	C	G	4: 21,679,659 (GRCm39)	R277P	unknown	Het
Prf1	A	C	10: 61,136,216 (GRCm39)	D164A	probably damaging	Het
Rarres1	A	G	3: 67,386,924 (GRCm39)	V226A	probably damaging	Het
Rest	GGGGGCCTGCCCCTCCCACGGGGCCTGCCCCTCCCACGGGGCCTGCCCCTCCCACGGAGCCTGCCCCTCCCACGGGGC	GGGGGCCTGCCCCTCCCACGGGGCCTGCCCCTCCCACGGAGCCTGCCCCTCCCACGGGGC	5: 77,429,651 (GRCm39)		probably benign	Het
Rnf123	A	G	9: 107,948,375 (GRCm39)	L106P	probably damaging	Het
Scnn1b	A	T	7: 121,511,326 (GRCm39)	T338S	probably benign	Het
Sfi1	A	ATCTTCCCAAAGCCAGTGC	11: 3,103,384 (GRCm39)		probably benign	Het
Slc9a5	T	C	8: 106,080,139 (GRCm39)	V94A	probably damaging	Het
Slco4a1	A	G	2: 180,106,478 (GRCm39)	D220G	probably benign	Het
Spata31e2	T	A	1: 26,723,485 (GRCm39)	Q565L	possibly damaging	Het
Sult1c2	T	C	17: 54,269,200 (GRCm39)	D272G	possibly damaging	Het
Tgm1	T	C	14: 55,946,355 (GRCm39)	N427S	probably damaging	Het
Themis	C	A	10: 28,658,233 (GRCm39)	T420N	probably benign	Het
Tnni3	A	T	7: 4,521,376 (GRCm39)	F209L	probably damaging	Het
Ttn	T	A	2: 76,745,912 (GRCm39)	S5046C	probably damaging	Het
Tubb2a	T	A	13: 34,260,628 (GRCm39)	I24L	probably benign	Het
Uevld	C	A	7: 46,587,746 (GRCm39)	G318V	probably damaging	Het
Unkl	T	C	17: 25,448,350 (GRCm39)	S308P	probably benign	Het
Vmn1r159	C	A	7: 22,542,765 (GRCm39)	C89F	probably damaging	Het
Wee2	T	G	6: 40,437,977 (GRCm39)	S302A	probably benign	Het
Ydjc	T	C	16: 16,965,666 (GRCm39)	C144R	probably benign	Het
Zc3h12c	A	G	9: 52,027,419 (GRCm39)	S667P	probably benign	Het
Zfp280b	T	A	10: 75,874,651 (GRCm39)	Y177N	probably benign	Het
Zfp354b	C	T	11: 50,814,362 (GRCm39)	E188K	probably benign	Het

Other mutations in Large1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00095:Large1	APN	8	73,564,125 (GRCm39)	missense	probably damaging	1.00
IGL00326:Large1	APN	8	73,858,611 (GRCm39)	missense	probably benign
IGL00418:Large1	APN	8	73,550,469 (GRCm39)	critical splice acceptor site	probably null
IGL01155:Large1	APN	8	73,858,617 (GRCm39)	missense	probably benign	0.01
IGL01793:Large1	APN	8	73,585,809 (GRCm39)	splice site	probably benign
IGL01929:Large1	APN	8	73,585,903 (GRCm39)	missense	probably damaging	1.00
IGL02218:Large1	APN	8	73,638,750 (GRCm39)	missense	probably damaging	1.00
IGL02276:Large1	APN	8	73,544,721 (GRCm39)	missense	probably benign	0.00
IGL02329:Large1	APN	8	73,774,945 (GRCm39)	missense	possibly damaging	0.80
IGL02543:Large1	APN	8	73,775,042 (GRCm39)	missense	probably benign	0.00
IGL02887:Large1	APN	8	73,858,667 (GRCm39)	missense	probably benign	0.07
biggs	UTSW	8	73,843,047 (GRCm39)	missense	probably damaging	1.00
umber	UTSW	8	73,609,892 (GRCm39)	nonsense	probably null
R0179:Large1	UTSW	8	73,825,474 (GRCm39)	missense	probably benign	0.09
R0477:Large1	UTSW	8	73,544,710 (GRCm39)	missense	probably damaging	1.00
R0587:Large1	UTSW	8	73,585,961 (GRCm39)	missense	probably damaging	1.00
R0791:Large1	UTSW	8	73,775,107 (GRCm39)	splice site	probably benign
R1253:Large1	UTSW	8	73,775,050 (GRCm39)	missense	probably damaging	0.98
R1695:Large1	UTSW	8	73,544,710 (GRCm39)	missense	probably damaging	1.00
R2017:Large1	UTSW	8	73,578,825 (GRCm39)	missense	probably damaging	1.00
R4835:Large1	UTSW	8	73,774,975 (GRCm39)	missense	probably damaging	1.00
R5105:Large1	UTSW	8	73,578,872 (GRCm39)	nonsense	probably null
R5120:Large1	UTSW	8	73,585,969 (GRCm39)	missense	probably damaging	1.00
R5135:Large1	UTSW	8	73,544,724 (GRCm39)	missense	probably benign	0.38
R5137:Large1	UTSW	8	73,774,937 (GRCm39)	missense	possibly damaging	0.58
R5567:Large1	UTSW	8	73,564,081 (GRCm39)	missense	possibly damaging	0.93
R5945:Large1	UTSW	8	73,578,828 (GRCm39)	missense	probably damaging	0.99
R6619:Large1	UTSW	8	73,609,892 (GRCm39)	nonsense	probably null
R6951:Large1	UTSW	8	73,843,047 (GRCm39)	missense	probably damaging	1.00
R7041:Large1	UTSW	8	73,843,092 (GRCm39)	missense	probably damaging	0.98
R7300:Large1	UTSW	8	73,564,224 (GRCm39)	missense	probably damaging	1.00
R7493:Large1	UTSW	8	73,550,343 (GRCm39)	missense	probably benign	0.23
R7877:Large1	UTSW	8	73,843,071 (GRCm39)	missense	probably damaging	1.00
R8118:Large1	UTSW	8	73,858,572 (GRCm39)	missense	probably benign	0.40
R8129:Large1	UTSW	8	73,542,585 (GRCm39)	missense	probably damaging	1.00
R8525:Large1	UTSW	8	73,564,120 (GRCm39)	missense	probably damaging	1.00
R8963:Large1	UTSW	8	73,542,612 (GRCm39)	missense	probably damaging	1.00
R9653:Large1	UTSW	8	73,564,106 (GRCm39)	missense	probably benign
Z1088:Large1	UTSW	8	73,638,731 (GRCm39)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- CTGTGAGATATTTCAAGGCAGC -3'
(R):5'- TATATGGAGAGCCGCTGGAG -3'

Sequencing Primer
(F):5'- CAAAGCCATATCGTCGGGACATG -3'
(R):5'- CCCATAAAGTATGAGTTTTACCCTC -3'

Posted On

2022-02-07