Mutagenetix > Incidental Mutation

Incidental Mutation 'R0416:Cd74'

40354

Institutional Source

Beutler Lab

Gene Symbol

Cd74

Ensembl Gene

ENSMUSG00000024610

Gene Name

CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)

Synonyms

CLIP, Ii

MMRRC Submission

038618-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.116) question?

Stock #

R0416 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

60936921-60945724 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 60944486 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Phenylalanine at position 232 (Y232F)

Ref Sequence

ENSEMBL: ENSMUSP00000126688 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000050487] [ENSMUST00000097563] [ENSMUST00000163446] [ENSMUST00000167610] [ENSMUST00000175934] [ENSMUST00000176630]

AlphaFold

P04441

Predicted Effect

probably benign
Transcript: ENSMUST00000050487

SMART Domains

Protein: ENSMUSP00000057836
Gene: ENSMUSG00000024610

Domain	Start	End	E-Value	Type
Pfam:MHC2-interact	1	112	2.8e-40	PFAM
Pfam:MHCassoc_trimer	119	190	6e-36	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000097563
AA Change: Y232F

PolyPhen 2 Score 0.902 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000095171
Gene: ENSMUSG00000024610
AA Change: Y232F

Domain	Start	End	E-Value	Type
Pfam:MHC2-interact	1	112	5.3e-40	PFAM
Pfam:MHCassoc_trimer	119	190	6.7e-36	PFAM
TY	212	258	8.6e-18	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000163446

SMART Domains

Protein: ENSMUSP00000130454
Gene: ENSMUSG00000024613

Domain	Start	End	E-Value	Type
LisH	6	38	5.09e-4	SMART
Pfam:Treacle	108	322	2.2e-8	PFAM
Pfam:Treacle	321	793	4.6e-204	PFAM
low complexity region	819	834	N/A	INTRINSIC
low complexity region	855	874	N/A	INTRINSIC
low complexity region	879	893	N/A	INTRINSIC
low complexity region	916	927	N/A	INTRINSIC
low complexity region	967	977	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000167610
AA Change: Y232F

PolyPhen 2 Score 0.902 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000126688
Gene: ENSMUSG00000024610
AA Change: Y232F

Domain	Start	End	E-Value	Type
Pfam:MHC2-interact	1	112	5.8e-45	PFAM
Pfam:MHCassoc_trimer	119	187	1.7e-34	PFAM
TY	212	258	8.6e-18	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175586

Predicted Effect

probably benign
Transcript: ENSMUST00000175934

SMART Domains

Protein: ENSMUSP00000135639
Gene: ENSMUSG00000024613

Domain	Start	End	E-Value	Type
LisH	6	38	5.09e-4	SMART
low complexity region	75	109	N/A	INTRINSIC
Pfam:Treacle	153	329	1.6e-12	PFAM
Pfam:Treacle	321	792	6.1e-175	PFAM
Pfam:Treacle	782	936	3.2e-16	PFAM
low complexity region	969	982	N/A	INTRINSIC
low complexity region	1025	1039	N/A	INTRINSIC
low complexity region	1060	1074	N/A	INTRINSIC
low complexity region	1149	1172	N/A	INTRINSIC
low complexity region	1260	1285	N/A	INTRINSIC
coiled coil region	1306	1335	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000176630

SMART Domains

Protein: ENSMUSP00000135476
Gene: ENSMUSG00000024613

Domain	Start	End	E-Value	Type
LisH	6	38	5.09e-4	SMART
Pfam:Treacle	108	323	2.5e-8	PFAM
Pfam:Treacle	321	793	5.9e-204	PFAM
low complexity region	819	834	N/A	INTRINSIC
low complexity region	843	857	N/A	INTRINSIC
low complexity region	880	891	N/A	INTRINSIC
low complexity region	933	946	N/A	INTRINSIC
low complexity region	989	1003	N/A	INTRINSIC
low complexity region	1024	1038	N/A	INTRINSIC
low complexity region	1113	1136	N/A	INTRINSIC
low complexity region	1224	1249	N/A	INTRINSIC
coiled coil region	1270	1299	N/A	INTRINSIC

Meta Mutation Damage Score

0.2462

Coding Region Coverage

1x: 99.1%
3x: 98.2%
10x: 96.2%
20x: 91.8%

Validation Efficiency

99% (74/75)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene associates with class II major histocompatibility complex (MHC) and is an important chaperone that regulates antigen presentation for immune response. It also serves as cell surface receptor for the cytokine macrophage migration inhibitory factor (MIF) which, when bound to the encoded protein, initiates survival pathways and cell proliferation. This protein also interacts with amyloid precursor protein (APP) and suppresses the production of amyloid beta (Abeta). Multiple alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Aug 2011]
PHENOTYPE: Homozygotes for targeted null mutations exhibit impaired transport of MHC class II molecules, poor antigen presentation, and deficiency of CD4+ T cell development and positive selection. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acsm2	A	G	7: 119,162,779 (GRCm39)	I18V	probably benign	Het
Adamdec1	T	G	14: 68,806,161 (GRCm39)	E438A	possibly damaging	Het
Adamts17	A	G	7: 66,565,646 (GRCm39)		probably null	Het
Ankrd44	T	G	1: 54,782,498 (GRCm39)	I359L	possibly damaging	Het
Ap2s1	C	A	7: 16,481,290 (GRCm39)	N86K	probably damaging	Het
Arih1	T	A	9: 59,333,993 (GRCm39)		probably benign	Het
Astn1	T	A	1: 158,337,461 (GRCm39)	I389N	probably damaging	Het
Brca2	T	C	5: 150,492,857 (GRCm39)	S3291P	possibly damaging	Het
Cacna1d	T	C	14: 29,822,645 (GRCm39)		probably benign	Het
Ccl7	C	A	11: 81,936,692 (GRCm39)		probably benign	Het
Cep128	A	G	12: 91,197,641 (GRCm39)		probably benign	Het
Cep89	T	A	7: 35,115,827 (GRCm39)		probably benign	Het
Cmya5	T	G	13: 93,226,364 (GRCm39)	N2908T	probably benign	Het
Coil	T	C	11: 88,872,812 (GRCm39)	L391S	possibly damaging	Het
Cpd	C	T	11: 76,676,030 (GRCm39)	V1208I	probably benign	Het
Ddx19a	T	C	8: 111,705,689 (GRCm39)	D254G	probably damaging	Het
Desi2	T	A	1: 178,083,887 (GRCm39)		probably benign	Het
Dnah11	A	T	12: 117,874,793 (GRCm39)	M4024K	probably damaging	Het
Ergic2	A	T	6: 148,084,642 (GRCm39)	L53H	probably damaging	Het
Etv2	T	C	7: 30,334,058 (GRCm39)	Y225C	probably benign	Het
F10	G	A	8: 13,105,448 (GRCm39)	A338T	probably damaging	Het
Fam228b	T	A	12: 4,812,382 (GRCm39)	D132V	probably damaging	Het
Fat2	T	A	11: 55,174,960 (GRCm39)	I1918F	possibly damaging	Het
Fbxw5	C	T	2: 25,393,251 (GRCm39)	S214F	probably damaging	Het
Glyat	G	A	19: 12,628,817 (GRCm39)	R204Q	possibly damaging	Het
Gm4825	T	C	15: 85,395,182 (GRCm39)		noncoding transcript	Het
Ino80d	G	T	1: 63,125,435 (GRCm39)	T9K	possibly damaging	Het
Lifr	A	T	15: 7,196,395 (GRCm39)	D193V	probably damaging	Het
Lrp12	G	T	15: 39,742,307 (GRCm39)		probably benign	Het
Lrp3	A	G	7: 34,901,778 (GRCm39)	V701A	probably benign	Het
Mfsd11	T	A	11: 116,756,708 (GRCm39)		probably benign	Het
Mrto4	A	T	4: 139,077,043 (GRCm39)		probably null	Het
Msi1	T	C	5: 115,568,708 (GRCm39)	F43L	possibly damaging	Het
Mthfsd	T	C	8: 121,827,976 (GRCm39)	D168G	probably damaging	Het
Myo15a	T	A	11: 60,402,000 (GRCm39)	V3099E	probably damaging	Het
Myrf	T	C	19: 10,193,176 (GRCm39)		probably null	Het
Nadk	C	A	4: 155,672,256 (GRCm39)		probably benign	Het
Nav1	T	C	1: 135,398,864 (GRCm39)	K573E	possibly damaging	Het
Ndufs3	A	G	2: 90,728,732 (GRCm39)	V207A	probably damaging	Het
Nlrp3	T	C	11: 59,446,750 (GRCm39)		probably benign	Het
Nlrx1	T	G	9: 44,174,211 (GRCm39)	D330A	probably benign	Het
Or2a56	G	A	6: 42,932,504 (GRCm39)	C24Y	probably benign	Het
Or2t49	T	C	11: 58,393,222 (GRCm39)	I53M	unknown	Het
Osbpl3	C	T	6: 50,324,998 (GRCm39)	V167I	probably benign	Het
Pcnx1	A	T	12: 82,021,240 (GRCm39)	I1410F	probably benign	Het
Piezo2	G	A	18: 63,157,562 (GRCm39)	R2383C	probably damaging	Het
Pip5kl1	A	T	2: 32,473,436 (GRCm39)	K358*	probably null	Het
Polg	T	C	7: 79,101,988 (GRCm39)		probably benign	Het
Prr14l	T	A	5: 32,986,061 (GRCm39)	I1145F	probably benign	Het
Psmb1	C	T	17: 15,714,781 (GRCm39)	V39I	probably benign	Het
Ptk6	T	C	2: 180,844,101 (GRCm39)	Y66C	possibly damaging	Het
Robo4	T	C	9: 37,316,062 (GRCm39)		probably benign	Het
Sdk2	A	G	11: 113,694,029 (GRCm39)	Y1801H	probably damaging	Het
Serpinb3a	C	A	1: 106,977,116 (GRCm39)	A95S	probably benign	Het
Setd1a	CTGGTGGTGGTGGTGGTGGTAGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGG	CTGGTGGTGGTGGTGGTAGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGG	7: 127,384,469 (GRCm39)		probably benign	Het
Sik2	A	T	9: 50,906,932 (GRCm39)	Y98N	probably damaging	Het
Slc30a1	C	T	1: 191,641,838 (GRCm39)	P495S	probably benign	Het
Smg1	A	T	7: 117,783,684 (GRCm39)		probably benign	Het
Stk3	T	A	15: 35,114,778 (GRCm39)	I45L	probably benign	Het
Tapbp	A	G	17: 34,144,392 (GRCm39)	T163A	probably damaging	Het
Tdrd5	T	C	1: 156,113,051 (GRCm39)	K410E	probably damaging	Het
Trim30b	A	T	7: 104,012,973 (GRCm39)	M152K	probably benign	Het
Trpm6	G	T	19: 18,760,389 (GRCm39)		probably benign	Het
Tsc22d1	T	C	14: 76,742,743 (GRCm39)		probably benign	Het
U2surp	A	T	9: 95,367,660 (GRCm39)	F444I	probably damaging	Het
Vmn2r95	C	T	17: 18,661,664 (GRCm39)	P470L	probably damaging	Het
Zc3h4	T	G	7: 16,154,200 (GRCm39)	Y163D	probably damaging	Het
Zfp62	A	T	11: 49,106,503 (GRCm39)	H198L	probably damaging	Het
Zmym1	A	G	4: 126,952,613 (GRCm39)	L56P	probably benign	Het

Other mutations in Cd74

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00980:Cd74	APN	18	60,944,398 (GRCm39)	missense	probably benign	0.02
IGL01475:Cd74	APN	18	60,943,393 (GRCm39)	unclassified	probably benign
IGL01867:Cd74	APN	18	60,941,352 (GRCm39)	missense	probably benign	0.03
IGL03207:Cd74	APN	18	60,944,996 (GRCm39)	unclassified	probably benign
R0010:Cd74	UTSW	18	60,936,968 (GRCm39)	start gained	probably benign
R0010:Cd74	UTSW	18	60,942,143 (GRCm39)	missense	probably benign	0.06
R0010:Cd74	UTSW	18	60,942,143 (GRCm39)	missense	probably benign	0.06
R0652:Cd74	UTSW	18	60,944,957 (GRCm39)	missense	probably damaging	1.00
R1433:Cd74	UTSW	18	60,937,064 (GRCm39)	missense	probably benign	0.04
R1490:Cd74	UTSW	18	60,944,438 (GRCm39)	missense	probably damaging	1.00
R1762:Cd74	UTSW	18	60,944,390 (GRCm39)	missense	probably benign	0.00
R1869:Cd74	UTSW	18	60,943,484 (GRCm39)	missense	probably benign	0.18
R4957:Cd74	UTSW	18	60,942,109 (GRCm39)	missense	probably benign	0.01
R5433:Cd74	UTSW	18	60,940,993 (GRCm39)	missense	probably benign	0.21
R5513:Cd74	UTSW	18	60,944,377 (GRCm39)	missense	probably damaging	1.00
R6073:Cd74	UTSW	18	60,944,558 (GRCm39)	critical splice donor site	probably null
R6381:Cd74	UTSW	18	60,944,435 (GRCm39)	missense	probably damaging	1.00
R7394:Cd74	UTSW	18	60,936,965 (GRCm39)	start gained	probably benign
R8944:Cd74	UTSW	18	60,943,127 (GRCm39)	missense	probably damaging	1.00
R9252:Cd74	UTSW	18	60,941,364 (GRCm39)	missense	possibly damaging	0.50
R9256:Cd74	UTSW	18	60,944,366 (GRCm39)	missense	probably benign	0.03
X0011:Cd74	UTSW	18	60,944,559 (GRCm39)	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- TTCACTGGGGCAAATGACACCTATAAG -3'
(R):5'- TGTATACTGGGAGGGACCTTTGGAC -3'

Sequencing Primer
(F):5'- ACTGGTTTCAGACTCAGGC -3'
(R):5'- AGGGACCTTTGGACCCTTG -3'

Posted On

2013-05-23