Mutagenetix > Incidental Mutation

Incidental Mutation 'R1869:Cd74'

210602

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

Ii, CLIP

MMRRC Submission

039891-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.188) question?

Stock #

R1869 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

60803848-60812646 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 60810412 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Proline to Serine at position 190 (P190S)

Ref Sequence

ENSEMBL: ENSMUSP00000126688 (fasta)

Gene Model

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

AlphaFold

P04441

Predicted Effect

probably benign
Transcript: ENSMUST00000050487
AA Change: P190S

PolyPhen 2 Score 0.184 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000057836
Gene: ENSMUSG00000024610
AA Change: P190S

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

probably benign
Transcript: ENSMUST00000097563
AA Change: P190S

PolyPhen 2 Score 0.184 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000095171
Gene: ENSMUSG00000024610
AA Change: P190S

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: ENSMUST00000167610
AA Change: P190S

PolyPhen 2 Score 0.184 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000126688
Gene: ENSMUSG00000024610
AA Change: P190S

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

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 95.4%
20x: 92.9%

Validation Efficiency

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: 127 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921536K21Rik	A	G	11: 3,890,067	L110P	probably damaging	Het
6030458C11Rik	T	C	15: 12,817,907	D168G	probably damaging	Het
Abca13	A	T	11: 9,292,134	E1332D	probably benign	Het
Abhd11	A	G	5: 135,011,617	Y168C	probably damaging	Het
Actr5	A	C	2: 158,638,723	T554P	probably damaging	Het
Adamts16	A	G	13: 70,735,747	L1103P	probably damaging	Het
Adgrb3	A	T	1: 25,826,438	I108K	possibly damaging	Het
Agbl4	T	A	4: 111,566,629	M284K	possibly damaging	Het
Aoc3	T	A	11: 101,331,467	Y176*	probably null	Het
Aox1	A	G	1: 58,076,103	E749G	probably damaging	Het
Ap4b1	T	A	3: 103,820,868	Y399*	probably null	Het
Arhgef5	A	T	6: 43,288,682	I1553F	probably damaging	Het
Bag6	T	C	17: 35,142,826	V541A	probably benign	Het
Bdp1	A	C	13: 100,042,201	V1879G	probably damaging	Het
Bod1l	G	A	5: 41,833,675	S179F	possibly damaging	Het
Bsnd	C	T	4: 106,486,636	V158I	probably benign	Het
Cachd1	C	A	4: 100,983,390	H880N	probably damaging	Het
Ccdc27	T	C	4: 154,026,763		probably null	Het
Cep68	A	T	11: 20,240,217	L265Q	probably damaging	Het
Cfap70	G	A	14: 20,408,610	Q772*	probably null	Het
CK137956	T	A	4: 127,970,534	S101C	possibly damaging	Het
Clca3a2	G	A	3: 144,806,403	T524M	probably benign	Het
Cxcr6	T	C	9: 123,809,957	S15P	probably benign	Het
Cyfip2	T	A	11: 46,224,168	Y904F	probably benign	Het
D130040H23Rik	T	A	8: 69,302,702	I253N	probably benign	Het
Ddx56	C	T	11: 6,263,993	V389M	possibly damaging	Het
Dmp1	A	T	5: 104,212,076	D206V	probably damaging	Het
Dnah17	A	T	11: 118,047,189	C3350*	probably null	Het
Dpcr1	A	G	17: 35,638,413	L98P	possibly damaging	Het
Dst	A	T	1: 34,252,832	S877C	probably damaging	Het
Ermp1	A	G	19: 29,646,015	S192P	possibly damaging	Het
F13b	G	A	1: 139,510,934	D359N	probably benign	Het
Fam171a1	A	T	2: 3,226,152	Q769L	possibly damaging	Het
Fap	T	C	2: 62,528,727	R411G	probably damaging	Het
Fbn1	A	G	2: 125,352,027	V1340A	probably benign	Het
Fbxw19	T	C	9: 109,482,032	I370V	probably benign	Het
Foxi1	A	T	11: 34,207,937	N29K	possibly damaging	Het
Frem2	T	G	3: 53,535,196	D2640A	probably benign	Het
Fzd4	T	C	7: 89,407,246	V167A	probably benign	Het
Galnt3	T	C	2: 66,097,779	I258V	possibly damaging	Het
Galr2	T	C	11: 116,283,243	V233A	possibly damaging	Het
Gldc	G	T	19: 30,139,332	Q407K	probably benign	Het
Gm5346	A	T	8: 43,625,095	Y697*	probably null	Het
Gmcl1	T	C	6: 86,697,516	D460G	probably benign	Het
Gpr89	A	G	3: 96,875,659	I325T	probably benign	Het
Grap	T	A	11: 61,664,189	Y61N	possibly damaging	Het
Hbs1l	G	T	10: 21,358,406		probably null	Het
Hexb	T	A	13: 97,191,259	E134D	probably benign	Het
Hydin	T	A	8: 110,500,705	V1507D	possibly damaging	Het
Igkv8-16	C	A	6: 70,386,987	G17V	probably benign	Het
Kdm4a	T	A	4: 118,138,871	Q987L	probably null	Het
Krt76	A	G	15: 101,889,487		probably null	Het
Lap3	T	C	5: 45,503,387	S238P	probably benign	Het
Letm2	T	C	8: 25,581,713	D391G	probably damaging	Het
Lipn	A	G	19: 34,080,739	T287A	possibly damaging	Het
Macf1	T	C	4: 123,351,128	S466G	probably damaging	Het
Map3k5	C	A	10: 20,132,109	S1220*	probably null	Het
Map4	T	C	9: 110,034,964	V419A	probably benign	Het
Map4	T	A	9: 110,068,928	S754R	possibly damaging	Het
Mroh9	A	G	1: 163,026,513	S773P	probably damaging	Het
Mtus1	A	C	8: 41,076,230		probably null	Het
Muc1	C	T	3: 89,231,810	P533S	probably damaging	Het
Muc13	A	T	16: 33,804,600	I282F	probably damaging	Het
Myh14	T	A	7: 44,611,643	Q1816L	possibly damaging	Het
Nalcn	A	C	14: 123,594,553	V103G	possibly damaging	Het
Nlrp9c	G	A	7: 26,384,820	Q445*	probably null	Het
Olfml2b	A	G	1: 170,669,243	D481G	probably damaging	Het
Olfr1000	A	G	2: 85,608,500	S137P	probably benign	Het
Olfr1087	T	A	2: 86,690,391	I195F	probably damaging	Het
Olfr309	T	A	7: 86,306,667	I149F	possibly damaging	Het
Olfr703	T	G	7: 106,845,094	I161S	probably benign	Het
Olfr884	T	A	9: 38,048,202		probably null	Het
Pcdhb2	A	T	18: 37,297,355		probably null	Het
Pcdhb22	A	C	18: 37,519,147	T223P	probably damaging	Het
Pcdhga1	T	A	18: 37,840,090	N907K	probably damaging	Het
Pcnt	T	C	10: 76,379,906	E2347G	probably null	Het
Phax	T	A	18: 56,573,104	V22D	probably benign	Het
Pik3ca	T	C	3: 32,450,350	F667S	probably damaging	Het
Pkd1	T	C	17: 24,594,931	F4123S	probably damaging	Het
Pkhd1	A	G	1: 20,615,267		probably null	Het
Plcb1	G	A	2: 135,311,014	R368K	probably benign	Het
Prrc2a	G	T	17: 35,153,308	R1739S	possibly damaging	Het
Psg23	A	T	7: 18,614,618	M88K	probably benign	Het
Pstk	T	A	7: 131,387,797	Y354N	probably damaging	Het
Rab39	A	G	9: 53,705,931	I62T	possibly damaging	Het
Ranbp2	A	G	10: 58,492,561	I2800V	probably damaging	Het
Rasgrp1	T	C	2: 117,290,347	Y431C	probably damaging	Het
Rest	T	A	5: 77,268,362	V141E	possibly damaging	Het
Rnf167	T	A	11: 70,650,139	I197N	possibly damaging	Het
Rtn1	A	G	12: 72,308,168	S335P	probably damaging	Het
Ryr2	G	T	13: 11,662,075	R3297S	probably damaging	Het
S1pr3	A	C	13: 51,419,916	K378Q	probably benign	Het
Scgb1b24	T	C	7: 33,744,044	Y43H	probably damaging	Het
Sh3rf3	T	A	10: 59,083,513	M484K	probably damaging	Het
Shank1	A	T	7: 44,342,115	R69*	probably null	Het
Siglecf	A	G	7: 43,355,543	N399S	probably benign	Het
Slc1a7	A	G	4: 108,008,364	T350A	probably damaging	Het
Slc25a54	T	A	3: 109,080,616	Y24*	probably null	Het
Slk	T	C	19: 47,625,452	F916L	probably damaging	Het
Snap91	T	A	9: 86,790,141		probably null	Het
Snrpb2	A	T	2: 143,065,186	R25S	possibly damaging	Het
Specc1l	T	C	10: 75,261,825	Y811H	probably damaging	Het
Sprr2h	A	G	3: 92,386,618		probably benign	Het
Sult2a5	A	T	7: 13,624,120	I26F	probably benign	Het
Syt13	C	T	2: 92,946,103	T245I	possibly damaging	Het
Tecrl	T	A	5: 83,354,859	T33S	probably benign	Het
Telo2	T	A	17: 25,114,994	D93V	probably benign	Het
Tet2	A	T	3: 133,481,441		probably null	Het
Tgm7	A	T	2: 121,101,089	C198S	probably damaging	Het
Ticrr	T	C	7: 79,679,135	F674S	probably damaging	Het
Tmem129	C	A	5: 33,654,499	C31F	probably damaging	Het
Tmem132a	T	A	19: 10,858,688	D826V	possibly damaging	Het
Tpd52	T	C	3: 8,953,802		probably null	Het
Trub2	A	G	2: 29,777,666	S321P	probably benign	Het
Ttc29	A	G	8: 78,282,385	T295A	probably benign	Het
Tubb1	G	A	2: 174,456,689	S89N	probably benign	Het
Ubap2	C	A	4: 41,233,617	G91V	probably damaging	Het
Ugt2b35	A	G	5: 87,001,288	N133D	probably damaging	Het
Usp34	A	G	11: 23,364,479	H807R	probably benign	Het
Vmn1r220	A	C	13: 23,184,287	C80G	probably damaging	Het
Vmn1r79	A	G	7: 12,176,647	E152G	probably benign	Het
Vmn2r28	T	C	7: 5,486,346	Y498C	probably benign	Het
Wif1	A	G	10: 121,084,919	I215M	probably benign	Het
Wnk1	T	C	6: 119,951,089	T1134A	probably damaging	Het
Zcchc11	T	A	4: 108,529,300	F1122L	probably damaging	Het
Zfp90	A	G	8: 106,419,123	H29R	probably benign	Het
Zfp972	A	G	2: 177,921,687		probably null	Het

Other mutations in Cd74

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00980:Cd74	APN	18	60811326	missense	probably benign	0.02
IGL01475:Cd74	APN	18	60810321	unclassified	probably benign
IGL01867:Cd74	APN	18	60808280	missense	probably benign	0.03
IGL03207:Cd74	APN	18	60811924	unclassified	probably benign
R0010:Cd74	UTSW	18	60803896	start gained	probably benign
R0010:Cd74	UTSW	18	60809071	missense	probably benign	0.06
R0010:Cd74	UTSW	18	60809071	missense	probably benign	0.06
R0416:Cd74	UTSW	18	60811414	missense	possibly damaging	0.90
R0652:Cd74	UTSW	18	60811885	missense	probably damaging	1.00
R1433:Cd74	UTSW	18	60803992	missense	probably benign	0.04
R1490:Cd74	UTSW	18	60811366	missense	probably damaging	1.00
R1762:Cd74	UTSW	18	60811318	missense	probably benign	0.00
R4957:Cd74	UTSW	18	60809037	missense	probably benign	0.01
R5433:Cd74	UTSW	18	60807921	missense	probably benign	0.21
R5513:Cd74	UTSW	18	60811305	missense	probably damaging	1.00
R6073:Cd74	UTSW	18	60811486	critical splice donor site	probably null
R6381:Cd74	UTSW	18	60811363	missense	probably damaging	1.00
R7394:Cd74	UTSW	18	60803893	start gained	probably benign
R8944:Cd74	UTSW	18	60810055	missense	probably damaging	1.00
R9252:Cd74	UTSW	18	60808292	missense	possibly damaging	0.50
R9256:Cd74	UTSW	18	60811294	missense	probably benign	0.03
X0011:Cd74	UTSW	18	60811487	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- GGGCCTTCTAACATTCACGAC -3'
(R):5'- CTCCAAGACAGAGAGCCTAGAG -3'

Sequencing Primer
(F):5'- AAGCTGGACCCCTCCAAGTTTG -3'
(R):5'- TAGAGGCCTCTGTACTCTGGAC -3'

Posted On

2014-06-30