Mutagenetix > Incidental Mutation

Incidental Mutation 'R4223:Galnt1'

319487

Institutional Source

Beutler Lab

Gene Symbol

Galnt1

Ensembl Gene

ENSMUSG00000000420

Gene Name

polypeptide N-acetylgalactosaminyltransferase 1

Synonyms

ppGaNTase-T1

MMRRC Submission

041043-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.911) question?

Stock #

R4223 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

24338401-24419873 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 24371413 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 4 (F4L)

Ref Sequence

ENSEMBL: ENSMUSP00000131755 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000000430] [ENSMUST00000164998] [ENSMUST00000170243] [ENSMUST00000171583] [ENSMUST00000178605]

AlphaFold

O08912

Predicted Effect

probably benign
Transcript: ENSMUST00000000430
AA Change: F4L

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

SMART Domains

Protein: ENSMUSP00000000430
Gene: ENSMUSG00000000420
AA Change: F4L

Domain	Start	End	E-Value	Type
transmembrane domain	7	29	N/A	INTRINSIC
Pfam:Glyco_tranf_2_3	116	369	3.2e-11	PFAM
Pfam:Glycos_transf_2	119	303	3.1e-40	PFAM
Pfam:Glyco_transf_7C	281	349	9.1e-10	PFAM
RICIN	426	551	1.25e-32	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000164998
AA Change: F4L

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000132411
Gene: ENSMUSG00000000420
AA Change: F4L

Domain	Start	End	E-Value	Type
transmembrane domain	10	29	N/A	INTRINSIC
PDB:1XHB\|A	88	142	1e-30	PDB
SCOP:d1qg8a_	116	141	6e-3	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000170243
AA Change: F4L

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

SMART Domains

Protein: ENSMUSP00000132142
Gene: ENSMUSG00000000420
AA Change: F4L

Domain	Start	End	E-Value	Type
transmembrane domain	7	29	N/A	INTRINSIC
Pfam:Glyco_tranf_2_3	116	369	1.7e-12	PFAM
Pfam:Glycos_transf_2	119	303	9.2e-37	PFAM
Pfam:Glyco_tranf_2_2	119	344	7.1e-7	PFAM
Pfam:Glyco_transf_7C	281	349	1.4e-8	PFAM
RICIN	426	551	1.25e-32	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000171583
AA Change: F4L

PolyPhen 2 Score 0.271 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000131755
Gene: ENSMUSG00000000420
AA Change: F4L

Domain	Start	End	E-Value	Type
transmembrane domain	10	29	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000178605
AA Change: F4L

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

SMART Domains

Protein: ENSMUSP00000137427
Gene: ENSMUSG00000000420
AA Change: F4L

Domain	Start	End	E-Value	Type
transmembrane domain	7	29	N/A	INTRINSIC
Pfam:Glyco_tranf_2_3	116	369	1.7e-12	PFAM
Pfam:Glycos_transf_2	119	303	9.2e-37	PFAM
Pfam:Glyco_tranf_2_2	119	344	7.1e-7	PFAM
Pfam:Glyco_transf_7C	281	349	1.4e-8	PFAM
RICIN	426	551	1.25e-32	SMART

Meta Mutation Damage Score

0.0665

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.6%

Validation Efficiency

98% (65/66)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase (GalNAc-T) family of enzymes. GalNAc-Ts initiate mucin-type O-linked glycosylation in the Golgi apparatus by catalyzing the transfer of GalNAc to serine and threonine residues on target proteins. They are characterized by an N-terminal transmembrane domain, a stem region, a lumenal catalytic domain containing a GT1 motif and Gal/GalNAc transferase motif, and a C-terminal ricin/lectin-like domain. GalNAc-Ts have different, but overlapping, substrate specificities and patterns of expression. Transcript variants derived from this gene that utilize alternative polyA signals have been described in the literature. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele exhibit some embryonic lethality, increased bleeding time, decreased T and B cells, impaired leukocyte rolling, decreased IgG levels, and hypoalbuminemia. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2610008E11Rik	A	G	10: 78,930,286 (GRCm39)	Y43H	probably damaging	Het
Aamp	A	T	1: 74,320,285 (GRCm39)	L348Q	probably damaging	Het
Abcb1b	T	A	5: 8,863,722 (GRCm39)	L226M	probably damaging	Het
Acap1	A	G	11: 69,774,511 (GRCm39)	S396P	probably damaging	Het
Aif1l	A	T	2: 31,852,251 (GRCm39)	S40C	probably damaging	Het
Atp1a3	T	C	7: 24,700,355 (GRCm39)	D48G	probably benign	Het
Bhmt-ps1	T	A	4: 26,369,352 (GRCm39)		noncoding transcript	Het
Ccdc116	A	G	16: 16,964,809 (GRCm39)		probably benign	Het
Cmtm5	T	A	14: 55,175,376 (GRCm39)	C51S	probably damaging	Het
Cyb5rl	T	C	4: 106,938,185 (GRCm39)	V214A	probably damaging	Het
Cyp4x1	A	T	4: 114,970,077 (GRCm39)	I350N	probably damaging	Het
Efcab6	C	A	15: 83,751,309 (GRCm39)	D1498Y	probably damaging	Het
Eif3c	C	G	7: 126,165,471 (GRCm39)		probably benign	Het
Epha3	G	A	16: 63,403,902 (GRCm39)	S733L	probably damaging	Het
Esyt1	T	C	10: 128,356,517 (GRCm39)	Y376C	probably damaging	Het
Glis1	T	C	4: 107,425,042 (GRCm39)	S218P	probably benign	Het
Gm15854	A	T	6: 129,949,426 (GRCm39)		noncoding transcript	Het
Gm29125	T	C	1: 80,361,236 (GRCm39)		noncoding transcript	Het
Inpp5a	T	C	7: 139,138,821 (GRCm39)	V263A	possibly damaging	Het
Itgb1	T	G	8: 129,440,624 (GRCm39)	I255S	probably damaging	Het
Kcp	A	G	6: 29,482,257 (GRCm39)	L1547P	possibly damaging	Het
Kifc3	C	A	8: 95,836,610 (GRCm39)	L72F	probably damaging	Het
Lama3	T	C	18: 12,583,460 (GRCm39)	C683R	probably damaging	Het
Lrrc55	G	A	2: 85,026,460 (GRCm39)	A188V	possibly damaging	Het
Ly6i	A	T	15: 74,854,884 (GRCm39)	S9T	probably benign	Het
Mfsd14b	C	T	13: 65,214,422 (GRCm39)		probably benign	Het
Nipsnap3a	T	A	4: 52,997,251 (GRCm39)	D172E	probably benign	Het
Or4g7	A	T	2: 111,309,489 (GRCm39)	Y120F	probably benign	Het
Oxgr1	T	C	14: 120,260,025 (GRCm39)	K61E	probably damaging	Het
Pak2	G	T	16: 31,871,028 (GRCm39)	N51K	probably benign	Het
Pcdhgb7	T	A	18: 37,886,856 (GRCm39)	D675E	probably benign	Het
Pcolce	T	A	5: 137,603,389 (GRCm39)		probably benign	Het
Phc3	A	T	3: 30,990,968 (GRCm39)	S383R	probably damaging	Het
Phf1	C	T	17: 27,156,474 (GRCm39)	R539*	probably null	Het
Plch1	G	A	3: 63,609,321 (GRCm39)	T48I	probably damaging	Het
Plekha2	A	G	8: 25,533,036 (GRCm39)	S312P	probably damaging	Het
Pnpla7	T	C	2: 24,872,126 (GRCm39)	F69L	possibly damaging	Het
Ppcdc	T	A	9: 57,321,998 (GRCm39)	M181L	possibly damaging	Het
Ptbp1	T	C	10: 79,695,047 (GRCm39)	I125T	probably benign	Het
Rfc3	C	A	5: 151,574,637 (GRCm39)		probably benign	Het
Rpa2	T	G	4: 132,504,055 (GRCm39)	I69S	probably damaging	Het
Rtn4	G	A	11: 29,656,856 (GRCm39)	V337I	probably benign	Het
Rttn	T	C	18: 89,113,708 (GRCm39)	L1709P	probably damaging	Het
Sh2b2	G	A	5: 136,247,907 (GRCm39)	P548L	possibly damaging	Het
Slc12a2	T	A	18: 58,043,328 (GRCm39)	S591T	probably damaging	Het
Slc25a45	A	T	19: 5,930,146 (GRCm39)	I39F	probably damaging	Het
Slc38a9	G	A	13: 112,850,782 (GRCm39)		probably null	Het
Slc9a4	T	C	1: 40,658,286 (GRCm39)	V603A	probably damaging	Het
Snx19	T	G	9: 30,339,744 (GRCm39)	V294G	possibly damaging	Het
Sp140l2	T	C	1: 85,090,278 (GRCm39)	D83G	probably damaging	Het
Sspo	G	T	6: 48,428,091 (GRCm39)	V313L	possibly damaging	Het
Stard9	A	G	2: 120,495,472 (GRCm39)	T116A	possibly damaging	Het
Strn3	C	T	12: 51,674,638 (GRCm39)	R382Q	probably damaging	Het
Trim43b	T	A	9: 88,972,692 (GRCm39)	Q154L	probably benign	Het
Trps1	A	G	15: 50,710,044 (GRCm39)	V98A	probably benign	Het
Vmn1r220	T	A	13: 23,368,148 (GRCm39)	M183L	probably benign	Het
Vmn2r60	A	T	7: 41,765,952 (GRCm39)	T20S	probably benign	Het
Wdr81	T	C	11: 75,338,828 (GRCm39)	T1444A	probably benign	Het
Xirp2	A	T	2: 67,346,837 (GRCm39)	E3026V	possibly damaging	Het

Other mutations in Galnt1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01833:Galnt1	APN	18	24,400,617 (GRCm39)	missense	probably damaging	1.00
IGL02373:Galnt1	APN	18	24,413,092 (GRCm39)	missense	possibly damaging	0.68
IGL02998:Galnt1	APN	18	24,397,469 (GRCm39)	missense	probably damaging	1.00
IGL03080:Galnt1	APN	18	24,402,574 (GRCm39)	missense	probably damaging	0.99
debonair	UTSW	18	24,404,686 (GRCm39)	missense	probably damaging	1.00
R0234:Galnt1	UTSW	18	24,387,690 (GRCm39)	missense	probably damaging	1.00
R0234:Galnt1	UTSW	18	24,387,690 (GRCm39)	missense	probably damaging	1.00
R0463:Galnt1	UTSW	18	24,387,582 (GRCm39)	missense	probably benign	0.01
R1183:Galnt1	UTSW	18	24,404,647 (GRCm39)	missense	probably damaging	1.00
R1954:Galnt1	UTSW	18	24,404,831 (GRCm39)	splice site	probably benign
R2349:Galnt1	UTSW	18	24,413,085 (GRCm39)	missense	probably benign	0.03
R3739:Galnt1	UTSW	18	24,404,712 (GRCm39)	missense	probably benign	0.27
R5001:Galnt1	UTSW	18	24,404,812 (GRCm39)	missense	probably benign
R5410:Galnt1	UTSW	18	24,400,604 (GRCm39)	missense	probably benign	0.02
R5516:Galnt1	UTSW	18	24,413,074 (GRCm39)	missense	probably benign	0.00
R5685:Galnt1	UTSW	18	24,397,586 (GRCm39)	missense	possibly damaging	0.81
R5687:Galnt1	UTSW	18	24,405,807 (GRCm39)	missense	probably benign	0.00
R5735:Galnt1	UTSW	18	24,397,577 (GRCm39)	missense	possibly damaging	0.64
R6106:Galnt1	UTSW	18	24,387,720 (GRCm39)	missense	probably benign	0.31
R6222:Galnt1	UTSW	18	24,397,591 (GRCm39)	critical splice donor site	probably null
R7448:Galnt1	UTSW	18	24,417,866 (GRCm39)	missense	probably benign	0.00
R7489:Galnt1	UTSW	18	24,415,214 (GRCm39)	missense	probably damaging	0.98
R8310:Galnt1	UTSW	18	24,404,686 (GRCm39)	missense	probably damaging	1.00
R8408:Galnt1	UTSW	18	24,400,628 (GRCm39)	missense	probably benign	0.44
R8884:Galnt1	UTSW	18	24,400,641 (GRCm39)	missense	probably benign	0.00
R8989:Galnt1	UTSW	18	24,402,567 (GRCm39)	missense	possibly damaging	0.55

Predicted Primers

PCR Primer
(F):5'- GCTTGATTGACTCTTACAGCTTTTG -3'
(R):5'- ATGACCAATCTCCTTAAGAAGACAG -3'

Sequencing Primer
(F):5'- TGAGACTGGAATAGTAGCTTACTGC -3'
(R):5'- TCTCCTTAAGAAGACAGCTGTAC -3'

Posted On

2015-06-10