Mutagenetix > Incidental Mutation

Incidental Mutation 'R8465:H2-D1'

656805

Institutional Source

Beutler Lab

Gene Symbol

H2-D1

Ensembl Gene

ENSMUSG00000073411

Gene Name

histocompatibility 2, D region locus 1

Synonyms

H-2D

MMRRC Submission

067909-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.097) question?

Stock #

R8465 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

35482070-35486473 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 35482487 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 69 (Y69C)

Ref Sequence

ENSEMBL: ENSMUSP00000134570 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000172785]

AlphaFold

no structure available at present

PDB Structure

CRYSTAL STRUCTURE OF MURINE CLASS I MHC H2-DB COMPLEXED WITH A SYNTHETIC PEPTIDE P1027 [X-RAY DIFFRACTION]
MHC CLASS I H-2DB COMPLEXED WITH A SENDAI VIRUS NUCLEOPROTEIN PEPTIDE [X-RAY DIFFRACTION]
CRYSTAL STRUCTURE OF MURINE CLASS I H-2DB COMPLEXED WITH PEPTIDE GP33(C9M) [X-RAY DIFFRACTION]
CRYSTAL STRUCTURE OF MURINE CLASS I H-2DB COMPLEXED WITH SYNTHETIC PEPTIDE GP33 (C9M/K1A) [X-RAY DIFFRACTION]
CRYSTAL STRUCTURE OF MURINE CLASS I H-2DB COMPLEXED WITH PEPTIDE GP33 (C9M/K1S) [X-RAY DIFFRACTION]
CRYSTAL STRUCTURE OF THE LCMV PEPTIDIC EPITOPE GP33 IN COMPLEX WITH THE MURINE CLASS I MHC MOLECULE H-2DB [X-RAY DIFFRACTION]
THE THREE-DIMENSIONAL STRUCTURE OF H-2DB AT 2.4 ANGSTROMS RESOLUTION: IMPLICATIONS FOR ANTIGEN-DETERMINANT SELECTION [X-RAY DIFFRACTION]
Structure of Minor Histocompatibility Antigen peptide, H13a, complexed to H2-Db [X-RAY DIFFRACTION]
Crystal Structure Of The LCMV Peptidic Epitope Gp276 In Complex With The Murine Class I Mhc Molecule H-2Db [X-RAY DIFFRACTION]
Crystal Structure Of The LCMV Peptidic Epitope Np396 In Complex With The Murine Class I Mhc Molecule H-2Db [X-RAY DIFFRACTION]
>> 46 additional structures at PDB <<

Predicted Effect

probably benign
Transcript: ENSMUST00000172503

SMART Domains

Protein: ENSMUSP00000134582
Gene: ENSMUSG00000073411

Domain	Start	End	E-Value	Type
SCOP:d1hdma1	2	21	3e-8	SMART
Pfam:MHC_I_C	57	81	1.9e-8	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000172785
AA Change: Y69C

PolyPhen 2 Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000134570
Gene: ENSMUSG00000073411
AA Change: Y69C

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
Pfam:MHC_I	25	203	8.3e-93	PFAM
IGc1	222	293	4.73e-23	SMART
transmembrane domain	308	330	N/A	INTRINSIC
Pfam:MHC_I_C	337	361	1e-8	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000173167

SMART Domains

Protein: ENSMUSP00000133518
Gene: ENSMUSG00000073411

Domain	Start	End	E-Value	Type
SCOP:d1hdma1	2	21	3e-8	SMART
Pfam:MHC_I_C	52	76	1.7e-8	PFAM

Meta Mutation Damage Score

0.6329

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

100% (80/80)

MGI Phenotype

PHENOTYPE: Mice homozygous for a spontaneous allele are susceptible to chronic Theiler's Murine Encephalomyelitis Virus (TMEV) infection and demyelination, and lack the ability to respond to the viral peptide VP2121-130, the single Ag driving the protective CD8 T cell response in wild-type B6 mice. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acot6	A	T	12: 84,153,215 (GRCm39)		probably null	Het
Adamtsl3	A	T	7: 82,247,330 (GRCm39)	N1429Y	probably benign	Het
Adk	T	C	14: 21,153,892 (GRCm39)	S32P	possibly damaging	Het
Akap13	A	T	7: 75,376,786 (GRCm39)	M2005L	probably benign	Het
Atp10a	A	T	7: 58,478,058 (GRCm39)	D1367V	probably benign	Het
Bckdhb	A	G	9: 83,870,915 (GRCm39)	I142V	probably benign	Het
Brap	C	T	5: 121,817,358 (GRCm39)	Q322*	probably null	Het
Carmil3	A	T	14: 55,734,305 (GRCm39)	N401I	probably damaging	Het
Cdan1	A	T	2: 120,558,921 (GRCm39)	S426T	possibly damaging	Het
Cdc27	C	A	11: 104,408,317 (GRCm39)	S531I	probably benign	Het
Cela3a	A	T	4: 137,131,185 (GRCm39)	Y184*	probably null	Het
Cep63	T	C	9: 102,490,576 (GRCm39)	K178R	probably benign	Het
Cfb	G	A	17: 35,076,290 (GRCm39)	Q152*	probably null	Het
Cnpy2	G	A	10: 128,162,044 (GRCm39)	V106I	probably benign	Het
Cntn1	GCTGTCTTC	GC	15: 92,237,404 (GRCm39)		probably null	Het
Ctc1	G	A	11: 68,917,045 (GRCm39)	G67D	probably damaging	Het
Cwc27	G	T	13: 104,940,772 (GRCm39)	P196T	probably benign	Het
Cwc27	C	A	13: 104,940,776 (GRCm39)	L194F	possibly damaging	Het
Cyp2d12	T	G	15: 82,439,378 (GRCm39)	S11A	possibly damaging	Het
Ddx55	T	A	5: 124,697,184 (GRCm39)		probably null	Het
Dedd2	G	T	7: 24,918,331 (GRCm39)	R75S	probably damaging	Het
Fat2	G	A	11: 55,147,530 (GRCm39)	S3904F	possibly damaging	Het
Fibp	G	A	19: 5,513,215 (GRCm39)	V177I	probably damaging	Het
Fsip2	A	T	2: 82,810,284 (GRCm39)	E2201V	probably benign	Het
Gbp11	C	T	5: 105,472,928 (GRCm39)	D499N	probably benign	Het
Gfm1	A	G	3: 67,339,032 (GRCm39)	E45G	probably damaging	Het
Hcar1	A	G	5: 124,017,109 (GRCm39)	F194S	probably damaging	Het
Heatr4	A	T	12: 84,024,707 (GRCm39)		probably null	Het
Kcnd2	G	A	6: 21,216,695 (GRCm39)	C133Y	probably damaging	Het
Kcnq1	A	T	7: 142,979,711 (GRCm39)	Q619L	probably benign	Het
Kctd12	T	A	14: 103,218,901 (GRCm39)	R326W	probably damaging	Het
Kel	A	G	6: 41,666,472 (GRCm39)		probably null	Het
Lipk	A	T	19: 34,024,197 (GRCm39)	I332F	probably benign	Het
Lrrc37	T	A	11: 103,506,947 (GRCm39)		probably benign	Het
Masp2	A	G	4: 148,696,516 (GRCm39)	D371G	possibly damaging	Het
Met	A	G	6: 17,571,809 (GRCm39)	E1376G	probably benign	Het
Mup5	A	T	4: 61,752,015 (GRCm39)	I78K	probably benign	Het
Mynn	A	T	3: 30,670,790 (GRCm39)	D526V	probably damaging	Het
Naip6	G	T	13: 100,433,423 (GRCm39)	T1138N	possibly damaging	Het
Neurod1	G	T	2: 79,284,696 (GRCm39)	P229Q	probably damaging	Het
Npepps	T	G	11: 97,139,085 (GRCm39)	R162S	probably damaging	Het
Ntrk3	T	A	7: 78,112,631 (GRCm39)	Q175L	probably damaging	Het
Obsl1	T	C	1: 75,480,032 (GRCm39)	T310A	probably damaging	Het
Or4g7	A	T	2: 111,309,425 (GRCm39)	T99S	probably benign	Het
Or8c9	A	T	9: 38,241,410 (GRCm39)	I176F	possibly damaging	Het
Or8j3c	A	T	2: 86,253,975 (GRCm39)	M15K	probably benign	Het
Or8k32	A	G	2: 86,368,731 (GRCm39)	I176T	probably damaging	Het
Pigf	G	A	17: 87,304,964 (GRCm39)	T193I	possibly damaging	Het
Pkp4	T	C	2: 59,172,525 (GRCm39)	V904A	possibly damaging	Het
Plekha6	C	T	1: 133,197,778 (GRCm39)	T141M	probably damaging	Het
Rapgef6	G	A	11: 54,582,308 (GRCm39)	D1407N	probably benign	Het
Rhobtb3	T	C	13: 76,087,741 (GRCm39)	D82G	probably damaging	Het
Rims1	T	C	1: 22,498,731 (GRCm39)	N767S	possibly damaging	Het
Ripor2	T	A	13: 24,849,451 (GRCm39)		probably benign	Het
Sec14l4	T	A	11: 3,993,948 (GRCm39)	I296N	probably damaging	Het
Serpinb12	G	T	1: 106,884,342 (GRCm39)	V363F	probably damaging	Het
Serpinb9c	A	G	13: 33,334,016 (GRCm39)	I342T	probably damaging	Het
Shmt2	A	G	10: 127,355,945 (GRCm39)	V133A	probably damaging	Het
Slc30a6	A	G	17: 74,722,661 (GRCm39)	M243V	probably benign	Het
Slfn2	T	A	11: 82,960,487 (GRCm39)	N155K	probably damaging	Het
Spata31h1	A	T	10: 82,152,298 (GRCm39)	L23M	possibly damaging	Het
Syne2	A	T	12: 75,900,898 (GRCm39)	D19V	possibly damaging	Het
Tcl1b3	A	T	12: 105,160,736 (GRCm39)	I116L	probably benign	Het
Tcp11	A	G	17: 28,286,766 (GRCm39)	I411T	probably damaging	Het
Tctn1	C	T	5: 122,379,859 (GRCm39)	A560T	probably benign	Het
Tenm3	C	A	8: 48,682,216 (GRCm39)	Q2471H	probably damaging	Het
Tnr	A	G	1: 159,713,645 (GRCm39)	D691G	probably benign	Het
Ube3b	C	T	5: 114,528,451 (GRCm39)	P150S	probably damaging	Het
Ugt2b5	T	C	5: 87,287,518 (GRCm39)	I216M	possibly damaging	Het
Unc5d	T	A	8: 29,156,877 (GRCm39)	R789S	probably damaging	Het
Ush2a	G	A	1: 188,147,875 (GRCm39)	G934D	probably damaging	Het
Usp6nl	A	T	2: 6,399,352 (GRCm39)	R70S	probably damaging	Het
Vmn1r181	T	C	7: 23,684,309 (GRCm39)	I258T	possibly damaging	Het
Vmn2r15	C	A	5: 109,445,302 (GRCm39)	D41Y	probably damaging	Het
Vmn2r17	T	A	5: 109,600,691 (GRCm39)	I663N	probably damaging	Het
Vnn3	C	A	10: 23,741,780 (GRCm39)	Q362K	possibly damaging	Het
Wdr72	A	G	9: 74,059,730 (GRCm39)	D380G	possibly damaging	Het
Wfdc10	G	A	2: 164,499,180 (GRCm39)	E97K	possibly damaging	Het
Xdh	A	T	17: 74,206,007 (GRCm39)	C1002*	probably null	Het
Zscan4e	A	C	7: 11,041,578 (GRCm39)	V126G	probably damaging	Het

Other mutations in H2-D1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02193:H2-D1	APN	17	35,484,785 (GRCm39)	missense	possibly damaging	0.91
IGL02207:H2-D1	APN	17	35,482,390 (GRCm39)	missense	possibly damaging	0.94
IGL02949:H2-D1	APN	17	35,483,064 (GRCm39)	missense	probably benign	0.02
Ancillum	UTSW	17	35,482,487 (GRCm39)	missense	probably damaging	0.98
subaltern	UTSW	17	35,482,913 (GRCm39)	missense	probably damaging	0.99
R0627:H2-D1	UTSW	17	35,484,898 (GRCm39)	missense	probably damaging	1.00
R0904:H2-D1	UTSW	17	35,482,837 (GRCm39)	missense	probably benign	0.00
R1238:H2-D1	UTSW	17	35,482,908 (GRCm39)	missense	probably damaging	1.00
R1500:H2-D1	UTSW	17	35,482,564 (GRCm39)	missense	probably benign	0.01
R1508:H2-D1	UTSW	17	35,482,844 (GRCm39)	missense	probably damaging	1.00
R1627:H2-D1	UTSW	17	35,482,471 (GRCm39)	missense	possibly damaging	0.79
R1730:H2-D1	UTSW	17	35,482,381 (GRCm39)	missense	probably damaging	1.00
R1804:H2-D1	UTSW	17	35,482,528 (GRCm39)	missense	probably damaging	1.00
R1964:H2-D1	UTSW	17	35,482,595 (GRCm39)	missense	probably benign	0.06
R2125:H2-D1	UTSW	17	35,483,091 (GRCm39)	critical splice donor site	probably null
R4652:H2-D1	UTSW	17	35,485,492 (GRCm39)	critical splice donor site	probably null
R4911:H2-D1	UTSW	17	35,484,973 (GRCm39)	missense	probably damaging	1.00
R4965:H2-D1	UTSW	17	35,482,881 (GRCm39)	missense	probably damaging	1.00
R5423:H2-D1	UTSW	17	35,484,883 (GRCm39)	missense	probably damaging	1.00
R6109:H2-D1	UTSW	17	35,482,913 (GRCm39)	missense	probably damaging	0.99
R7525:H2-D1	UTSW	17	35,484,909 (GRCm39)	missense	probably damaging	1.00
R7697:H2-D1	UTSW	17	35,482,121 (GRCm39)	missense	probably damaging	1.00
R7832:H2-D1	UTSW	17	35,482,848 (GRCm39)	missense	probably damaging	0.99
R7903:H2-D1	UTSW	17	35,482,967 (GRCm39)	missense	probably damaging	0.99
R8004:H2-D1	UTSW	17	35,485,672 (GRCm39)	missense	probably benign	0.00
R8167:H2-D1	UTSW	17	35,485,741 (GRCm39)	missense
R8786:H2-D1	UTSW	17	35,482,844 (GRCm39)	missense	probably damaging	1.00
R9188:H2-D1	UTSW	17	35,484,778 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGGTTATAAAGTCCACGCAACC -3'
(R):5'- TTCCCAAACCTCGGACTTGG -3'

Sequencing Primer
(F):5'- GACTCAGACACCCGGGATC -3'
(R):5'- AAACCTCGGACTTGGGACCC -3'

Posted On

2021-01-18