Mutagenetix > Incidental Mutation

Incidental Mutation 'R4957:Cd74'

381686

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

042554-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.152) question?

Stock #

R4957 (G1)

Quality Score

216

Status

Validated

Chromosome

Chromosomal Location

60803848-60812646 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 60809037 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Aspartic acid at position 113 (N113D)

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: N113D

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000057836
Gene: ENSMUSG00000024610
AA Change: N113D

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: N113D

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000095171
Gene: ENSMUSG00000024610
AA Change: N113D

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: N113D

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000126688
Gene: ENSMUSG00000024610
AA Change: N113D

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

0.0946

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.3%
20x: 92.5%

Validation Efficiency

99% (80/81)

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
3110009E18Rik	G	C	1: 120,169,110		probably benign	Het
3110009E18Rik	G	T	1: 120,169,119		probably benign	Het
3110009E18Rik	C	T	1: 120,169,120		probably benign	Het
6820408C15Rik	T	A	2: 152,444,093	V342D	probably damaging	Het
Arhgap33	C	T	7: 30,532,361	G101R	probably damaging	Het
Atf7ip	C	T	6: 136,606,810	R1280C	probably damaging	Het
Cacnb4	T	C	2: 52,558,291	H8R	probably damaging	Het
Ccdc150	T	A	1: 54,364,868		probably benign	Het
Cd163l1	T	C	7: 140,228,522	V782A	probably damaging	Het
Cdc25b	T	C	2: 131,193,605	V341A	possibly damaging	Het
Clptm1l	T	A	13: 73,611,196	I245N	possibly damaging	Het
Clptm1l	T	C	13: 73,612,428	I310T	probably damaging	Het
Creb5	A	T	6: 53,693,922		probably null	Het
Crebbp	T	C	16: 4,117,367	Q460R	probably benign	Het
Dnah17	A	T	11: 118,074,298	I2306N	probably benign	Het
Dync1h1	C	A	12: 110,658,126	T3700N	probably damaging	Het
Elovl1	A	T	4: 118,431,923	H215L	probably damaging	Het
Enkd1	A	G	8: 105,704,489	I202T	probably benign	Het
Epha7	C	T	4: 28,871,892	A407V	probably damaging	Het
Ercc3	G	T	18: 32,243,117	G130W	probably damaging	Het
Fbxl8	A	G	8: 105,268,195	E113G	probably damaging	Het
Frmpd1	T	G	4: 45,273,099	N339K	probably damaging	Het
Frrs1	G	A	3: 116,885,248	D240N	probably benign	Het
Gemin2	A	G	12: 59,017,168	S105G	probably benign	Het
Glra1	T	A	11: 55,527,398	I257F	probably damaging	Het
Gmcl1	G	A	6: 86,710,521	P354S	probably damaging	Het
Gpr15	G	T	16: 58,718,174	A184E	probably damaging	Het
Grm7	G	A	6: 111,358,863	G745E	probably damaging	Het
H2-T10	T	A	17: 36,117,416		probably benign	Het
Hdac5	C	A	11: 102,205,256		probably benign	Het
Ift22	G	A	5: 136,908,216		probably benign	Het
Ighg3	T	C	12: 113,361,130	E34G	unknown	Het
Itga11	A	T	9: 62,767,648	T821S	probably benign	Het
Lmod2	T	C	6: 24,603,872	V282A	possibly damaging	Het
Maml2	A	G	9: 13,620,276	K262R	probably damaging	Het
Mme	T	A	3: 63,343,489		probably benign	Het
Mnat1	A	G	12: 73,123,878	Y14C	probably damaging	Het
Mtdh	A	T	15: 34,083,135	T34S	possibly damaging	Het
Ncaph	T	C	2: 127,121,257	D352G	possibly damaging	Het
Olfr1014	T	C	2: 85,777,115	F177S	probably damaging	Het
Olfr1036	T	A	2: 86,075,510	Y257N	probably damaging	Het
Olfr1293-ps	C	A	2: 111,528,224	N321K	probably benign	Het
Olfr224	A	G	11: 58,566,518	Y276H	probably damaging	Het
Pcdhb13	T	A	18: 37,444,784	D738E	possibly damaging	Het
Pla2g4f	C	T	2: 120,300,499	R825Q	probably benign	Het
Pnliprp2	C	T	19: 58,775,145	L409F	possibly damaging	Het
Prlr	G	T	15: 10,319,195	C70F	probably damaging	Het
Ptpn14	C	T	1: 189,851,272	T772I	probably benign	Het
Ryr2	T	C	13: 11,785,080	Q927R	probably damaging	Het
Scarf1	A	G	11: 75,525,634	E634G	probably benign	Het
Slc39a14	A	T	14: 70,315,811	S158R	probably damaging	Het
Slc9c1	A	T	16: 45,544,831	T176S	probably benign	Het
Srsf10	T	C	4: 135,856,230	S2P	probably damaging	Het
Tcam1	T	A	11: 106,282,879	C50S	probably damaging	Het
Tcf7l2	A	G	19: 55,931,432		probably null	Het
Tdrd3	T	A	14: 87,505,787	H390Q	probably benign	Het
Tlk2	T	C	11: 105,253,359		probably null	Het
Tnc	G	C	4: 63,976,556	P1531R	probably damaging	Het
Tnfrsf1b	C	A	4: 145,246,757	Q15H	probably damaging	Het
Tnfrsf1b	T	G	4: 145,246,758	Q15P	possibly damaging	Het
Tssk4	A	T	14: 55,651,809	E264V	probably damaging	Het
Ttc37	T	G	13: 76,185,113		probably null	Het
Ugt3a2	G	A	15: 9,365,188	V296I	probably benign	Het
Usp5	C	G	6: 124,822,630	K318N	possibly damaging	Het
Vmn2r8	T	G	5: 108,799,263	E541A	probably benign	Het
Ybx1	A	T	4: 119,278,938		probably benign	Het
Zfp39	T	A	11: 58,891,231	Y235F	possibly damaging	Het
Zfp422	T	A	6: 116,626,943	K32*	probably null	Het
Zpbp2	T	A	11: 98,551,324		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
R1869:Cd74	UTSW	18	60810412	missense	probably benign	0.18
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'- TGCTATTGGGAAGGCTCTGAC -3'
(R):5'- TAGGGGATGGACTGTACGCAAC -3'

Sequencing Primer
(F):5'- AAGGCTCTGACAAGCTTCTG -3'
(R):5'- TGTACGCAACAGTTAAGGACC -3'

Posted On

2016-04-27