Mutagenetix > Incidental Mutation

Incidental Mutation 'R5026:Cd4'

475482

Institutional Source

Beutler Lab

Gene Symbol

Cd4

Ensembl Gene

ENSMUSG00000023274

Gene Name

CD4 antigen

Synonyms

L3T4, Ly-4

MMRRC Submission

042617-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5026 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

124864692-124888221 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 124866620 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 443 (T443A)

Ref Sequence

ENSEMBL: ENSMUSP00000024044 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000024044] [ENSMUST00000046893] [ENSMUST00000204667]

AlphaFold

P06332

Predicted Effect

possibly damaging
Transcript: ENSMUST00000024044
AA Change: T443A

PolyPhen 2 Score 0.955 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000024044
Gene: ENSMUSG00000023274
AA Change: T443A

Domain	Start	End	E-Value	Type
low complexity region	6	21	N/A	INTRINSIC
IGv	37	114	7.02e-8	SMART
IG	131	206	3.63e-1	SMART
IG	212	317	3.36e0	SMART
transmembrane domain	394	416	N/A	INTRINSIC
Pfam:Tcell_CD4_C	425	452	2.2e-18	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000046893

SMART Domains

Protein: ENSMUSP00000038536
Gene: ENSMUSG00000038390

Domain	Start	End	E-Value	Type
Pfam:7tm_1	30	337	1.1e-19	PFAM
low complexity region	348	362	N/A	INTRINSIC
low complexity region	462	477	N/A	INTRINSIC
low complexity region	482	504	N/A	INTRINSIC
low complexity region	513	540	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145818

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145977

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000151594

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000204161

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000204253

Predicted Effect

probably benign
Transcript: ENSMUST00000204667

SMART Domains

Protein: ENSMUSP00000145267
Gene: ENSMUSG00000038390

Domain	Start	End	E-Value	Type
Pfam:7tm_1	30	337	1.1e-19	PFAM
low complexity region	348	362	N/A	INTRINSIC
low complexity region	462	477	N/A	INTRINSIC
low complexity region	482	504	N/A	INTRINSIC
low complexity region	513	540	N/A	INTRINSIC

Meta Mutation Damage Score

0.0775

Coding Region Coverage

1x: 99.0%
3x: 98.2%
10x: 95.9%
20x: 90.7%

Validation Efficiency

96% (88/92)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a membrane glycoprotein of T lymphocytes that interacts with major histocompatibility complex class II antigenes and is also a receptor for the human immunodeficiency virus. This gene is expressed not only in T lymphocytes, but also in B cells, macrophages, and granulocytes. It is also expressed in specific regions of the brain. The protein functions to initiate or augment the early phase of T-cell activation, and may function as an important mediator of indirect neuronal damage in infectious and immune-mediated diseases of the central nervous system. Multiple alternatively spliced transcript variants encoding different isoforms have been identified in this gene. [provided by RefSeq, Aug 2010]
PHENOTYPE: Mice homozygous for knock-out alleles exhibit abnormal immune system morphology and physiology. [provided by MGI curators]

Allele List at MGI

All alleles(25) : Targeted(13) Gene trapped(6) Spontaneous(2) Chemically induced(4)

Other mutations in this stock

Total: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca12	T	C	1: 71,317,224 (GRCm38)	N608S	probably benign	Het
Actg1	T	C	11: 120,346,958 (GRCm38)	N7S	probably damaging	Het
Adamtsl3	T	A	7: 82,576,054 (GRCm38)	L357Q	probably benign	Het
Ahnak	A	T	19: 9,010,631 (GRCm38)	Q3093L	possibly damaging	Het
Ankrd16	T	A	2: 11,789,881 (GRCm38)	V359E	probably benign	Het
Ankrd40	T	C	11: 94,339,724 (GRCm38)		probably benign	Het
Ano10	G	A	9: 122,272,559 (GRCm38)	Q49*	probably null	Het
Aoah	A	T	13: 20,914,959 (GRCm38)	D236V	probably damaging	Het
Bin1	T	C	18: 32,419,930 (GRCm38)		probably null	Het
Braf	T	C	6: 39,688,287 (GRCm38)	D49G	probably benign	Het
Brsk1	A	T	7: 4,704,266 (GRCm38)	R273W	probably damaging	Het
C2cd3	T	A	7: 100,459,842 (GRCm38)	M2259K	possibly damaging	Het
Cabp1	T	C	5: 115,175,472 (GRCm38)	N43D	possibly damaging	Het
Ccar2	T	A	14: 70,142,502 (GRCm38)	Q412L	possibly damaging	Het
Cdh23	T	A	10: 60,304,848 (GRCm38)	I3206F	possibly damaging	Het
Ceacam9	A	T	7: 16,725,197 (GRCm38)		probably null	Het
Chid1	T	C	7: 141,513,836 (GRCm38)	D289G	probably damaging	Het
Chmp6	T	A	11: 119,918,643 (GRCm38)	L196Q	probably damaging	Het
Cog8	A	G	8: 107,049,125 (GRCm38)	S536P	probably benign	Het
Dmxl2	A	T	9: 54,416,676 (GRCm38)	S1141R	probably damaging	Het
Dnah7a	T	G	1: 53,662,498 (GRCm38)	Y166S	probably damaging	Het
Dnah7b	G	T	1: 46,187,363 (GRCm38)	W1318L	probably damaging	Het
Ecd	A	G	14: 20,337,030 (GRCm38)	F212S	probably damaging	Het
Entpd6	A	T	2: 150,763,644 (GRCm38)	S265C	probably damaging	Het
Epb41l2	A	G	10: 25,484,308 (GRCm38)	T523A	possibly damaging	Het
Focad	T	C	4: 88,344,582 (GRCm38)	S939P	unknown	Het
Gjb3	A	T	4: 127,326,487 (GRCm38)	V84D	probably damaging	Het
Gm572	A	T	4: 148,654,844 (GRCm38)	E43V	possibly damaging	Het
Gm6185	T	A	1: 161,224,608 (GRCm38)		noncoding transcript	Het
Gria1	T	A	11: 57,310,696 (GRCm38)	C787S	probably damaging	Het
Grpel2	A	G	18: 61,715,953 (GRCm38)	L162P	probably damaging	Het
Herc1	A	G	9: 66,486,126 (GRCm38)	T4096A	probably benign	Het
Hook3	A	T	8: 26,110,757 (GRCm38)	M41K	probably damaging	Het
Ifit1bl1	T	C	19: 34,593,893 (GRCm38)	Y388C	probably damaging	Het
Ighv3-4	A	G	12: 114,253,762 (GRCm38)	Y70H	probably benign	Het
Itm2c	T	C	1: 85,906,492 (GRCm38)	L176P	probably damaging	Het
Lmtk3	G	A	7: 45,794,412 (GRCm38)		probably benign	Het
Macf1	G	A	4: 123,439,494 (GRCm38)	T2376I	possibly damaging	Het
Map1a	T	G	2: 121,307,538 (GRCm38)	S2660A	possibly damaging	Het
Mmrn2	A	G	14: 34,399,201 (GRCm38)	H676R	probably benign	Het
Nbeal1	A	T	1: 60,237,179 (GRCm38)	K693M	probably damaging	Het
Ndufa13	T	A	8: 69,895,270 (GRCm38)	R49*	probably null	Het
Neb	T	A	2: 52,204,880 (GRCm38)	T1115S	possibly damaging	Het
Nvl	C	T	1: 181,105,155 (GRCm38)	R699H	probably damaging	Het
Or10w1	A	G	19: 13,654,932 (GRCm38)	I163V	probably benign	Het
Or5d47	A	T	2: 87,974,020 (GRCm38)	I215N	probably damaging	Het
Or8b53	A	G	9: 38,755,745 (GRCm38)	D19G	probably benign	Het
Or8d2b	A	T	9: 38,877,899 (GRCm38)	H241L	possibly damaging	Het
Piezo1	G	T	8: 122,486,818 (GRCm38)	D1779E	probably benign	Het
Prl8a9	A	G	13: 27,561,577 (GRCm38)	S77P	probably damaging	Het
Prune2	A	T	19: 17,199,142 (GRCm38)	I2904F	probably damaging	Het
Retreg1	T	A	15: 25,970,128 (GRCm38)	S151T	probably damaging	Het
Rnf213	A	G	11: 119,436,764 (GRCm38)	D1859G	probably damaging	Het
Rnf39	T	C	17: 36,945,534 (GRCm38)	F173L	probably benign	Het
Rspry1	T	A	8: 94,650,303 (GRCm38)	N371K	probably damaging	Het
Samd9l	T	A	6: 3,375,284 (GRCm38)	D659V	possibly damaging	Het
Sez6	T	A	11: 77,968,989 (GRCm38)	F378Y	probably damaging	Het
Slc22a19	G	A	19: 7,674,372 (GRCm38)	T490M	probably benign	Het
Slit2	A	T	5: 48,256,805 (GRCm38)	N917I	probably damaging	Het
Smg1	T	A	7: 118,193,545 (GRCm38)		probably benign	Het
Tes	T	C	6: 17,096,340 (GRCm38)	V24A	probably benign	Het
Tial1	C	T	7: 128,448,396 (GRCm38)	E82K	probably damaging	Het
Tmem94	G	A	11: 115,793,104 (GRCm38)	C750Y	probably damaging	Het
Tmppe	T	A	9: 114,405,819 (GRCm38)	N395K	possibly damaging	Het
Tnn	T	C	1: 160,146,137 (GRCm38)	H220R	probably benign	Het
Trappc10	T	C	10: 78,204,288 (GRCm38)	T610A	possibly damaging	Het
Trmt1l	T	A	1: 151,440,876 (GRCm38)	M196K	probably damaging	Het
Trpv4	T	C	5: 114,622,654 (GRCm38)	*872W	probably null	Het
Ttn	T	C	2: 76,749,009 (GRCm38)	T23847A	probably benign	Het
Ube4b	T	A	4: 149,360,565 (GRCm38)	L440F	probably damaging	Het
Ugt1a5	C	G	1: 88,166,241 (GRCm38)	R64G	probably benign	Het
Unc13c	T	A	9: 73,930,903 (GRCm38)	T889S	possibly damaging	Het
Vmn1r215	C	T	13: 23,076,279 (GRCm38)	T163I	probably benign	Het
Vmn2r16	T	A	5: 109,360,856 (GRCm38)	Y483*	probably null	Het
Wdr47	T	A	3: 108,618,522 (GRCm38)	C120*	probably null	Het
Zc3h6	G	A	2: 129,017,309 (GRCm38)	V1087I	probably benign	Het
Zfp423	T	C	8: 87,780,674 (GRCm38)	H889R	probably damaging	Het
Zfp825	G	T	13: 74,481,077 (GRCm38)	H107N	probably benign	Het
Zfp945	T	C	17: 22,850,885 (GRCm38)	H680R	probably damaging	Het

Other mutations in Cd4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
maat	APN	6	124,866,684 (GRCm38)	unclassified	probably benign
seshat	APN	6	124,872,977 (GRCm38)	missense	possibly damaging	0.81
thoth	APN	6	124,873,140 (GRCm38)	splice site	probably benign
IGL00783:Cd4	APN	6	124,872,989 (GRCm38)	missense	possibly damaging	0.81
IGL00784:Cd4	APN	6	124,872,989 (GRCm38)	missense	possibly damaging	0.81
IGL01294:Cd4	APN	6	124,879,378 (GRCm38)	missense	probably benign	0.41
IGL01295:Cd4	APN	6	124,879,378 (GRCm38)	missense	probably benign	0.41
IGL01296:Cd4	APN	6	124,879,378 (GRCm38)	missense	probably benign	0.41
IGL01298:Cd4	APN	6	124,879,378 (GRCm38)	missense	probably benign	0.41
IGL01299:Cd4	APN	6	124,879,378 (GRCm38)	missense	probably benign	0.41
IGL01397:Cd4	APN	6	124,879,378 (GRCm38)	missense	probably benign	0.41
IGL01401:Cd4	APN	6	124,879,378 (GRCm38)	missense	probably benign	0.41
IGL01402:Cd4	APN	6	124,879,378 (GRCm38)	missense	probably benign	0.41
IGL01407:Cd4	APN	6	124,879,378 (GRCm38)	missense	probably benign	0.41
craw	UTSW	6	124,867,746 (GRCm38)	nonsense	probably null
Doubles	UTSW	6	124,872,458 (GRCm38)	missense	probably benign	0.01
fourless	UTSW	6	124,870,244 (GRCm38)	critical splice donor site	probably null
R0152:Cd4	UTSW	6	124,867,746 (GRCm38)	nonsense	probably null
R0196:Cd4	UTSW	6	124,867,806 (GRCm38)	missense	probably damaging	0.97
R1769:Cd4	UTSW	6	124,866,655 (GRCm38)	missense	possibly damaging	0.71
R1992:Cd4	UTSW	6	124,867,688 (GRCm38)	missense	possibly damaging	0.59
R2126:Cd4	UTSW	6	124,870,536 (GRCm38)	missense	probably benign	0.01
R3237:Cd4	UTSW	6	124,867,670 (GRCm38)	missense	probably benign	0.37
R3706:Cd4	UTSW	6	124,879,388 (GRCm38)	missense	probably benign
R4535:Cd4	UTSW	6	124,870,451 (GRCm38)	missense	probably benign	0.01
R5084:Cd4	UTSW	6	124,870,439 (GRCm38)	missense	probably damaging	1.00
R6628:Cd4	UTSW	6	124,879,468 (GRCm38)	missense	unknown
R6772:Cd4	UTSW	6	124,872,458 (GRCm38)	missense	probably benign	0.01
R7038:Cd4	UTSW	6	124,870,254 (GRCm38)	missense	probably damaging	0.98
R7083:Cd4	UTSW	6	124,870,572 (GRCm38)	missense	probably benign	0.16
R7313:Cd4	UTSW	6	124,867,103 (GRCm38)	missense	probably benign	0.15
R7394:Cd4	UTSW	6	124,873,041 (GRCm38)	missense	probably benign	0.00
R7943:Cd4	UTSW	6	124,870,244 (GRCm38)	critical splice donor site	probably null
R9187:Cd4	UTSW	6	124,867,688 (GRCm38)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- ACATTGGTACCTCAGGGCAC -3'
(R):5'- AACAGATGTCACTGACAGGAC -3'

Sequencing Primer
(F):5'- TCTGTGCAGACCCAGAGG -3'
(R):5'- CAGGACGGGGGCTTAAGC -3'

Posted On

2017-04-28