Mutagenetix > Incidental Mutation

Incidental Mutation 'R2870:Cd6'

266554

Institutional Source

Beutler Lab

Gene Symbol

Cd6

Ensembl Gene

ENSMUSG00000024670

Gene Name

CD6 antigen

Synonyms

MMRRC Submission

040458-MU

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.070) question?

Stock #

R2870 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

10789341-10830058 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 10794626 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 307 (I307T)

Ref Sequence

ENSEMBL: ENSMUSP00000134639 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000039043] [ENSMUST00000080292] [ENSMUST00000174176]

AlphaFold

Q61003

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000025572

Predicted Effect

probably benign
Transcript: ENSMUST00000039043
AA Change: I408T

PolyPhen 2 Score 0.023 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000046861
Gene: ENSMUSG00000024670
AA Change: I408T

Domain	Start	End	E-Value	Type
signal peptide	1	17	N/A	INTRINSIC
SR	45	155	7.33e-9	SMART
SR	160	259	8.68e-52	SMART
SR	264	360	3.51e-29	SMART
low complexity region	383	394	N/A	INTRINSIC
transmembrane domain	400	422	N/A	INTRINSIC
low complexity region	569	582	N/A	INTRINSIC
low complexity region	611	623	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000080292
AA Change: I408T

PolyPhen 2 Score 0.023 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000079172
Gene: ENSMUSG00000024670
AA Change: I408T

Domain	Start	End	E-Value	Type
signal peptide	1	17	N/A	INTRINSIC
SR	45	155	7.33e-9	SMART
SR	160	259	8.68e-52	SMART
SR	264	360	3.51e-29	SMART
low complexity region	383	394	N/A	INTRINSIC
transmembrane domain	400	422	N/A	INTRINSIC
low complexity region	473	481	N/A	INTRINSIC
low complexity region	608	621	N/A	INTRINSIC
low complexity region	650	662	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173613

Predicted Effect

possibly damaging
Transcript: ENSMUST00000174176
AA Change: I307T

PolyPhen 2 Score 0.861 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000134639
Gene: ENSMUSG00000024670
AA Change: I307T

Domain	Start	End	E-Value	Type
signal peptide	1	17	N/A	INTRINSIC
SR	45	155	7.33e-9	SMART
SR	160	259	8.68e-52	SMART
low complexity region	282	293	N/A	INTRINSIC
transmembrane domain	299	321	N/A	INTRINSIC

Meta Mutation Damage Score

0.4887

Coding Region Coverage

1x: 99.1%
3x: 98.6%
10x: 97.3%
20x: 95.0%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein found on the outer membrane of T-lymphocytes as well as some other immune cells. The encoded protein contains three scavenger receptor cysteine-rich (SRCR) domains and a binding site for an activated leukocyte cell adhesion molecule. The gene product is important for continuation of T cell activation. This gene may be associated with susceptibility to multiple sclerosis (PMID: 19525953, 21849685). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit reduced susceptibility to insteinal ischemia/reperfusion induced injury due to reduced IgM-producing B1a cell self-renewal. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930444G20Rik	A	T	10: 22,067,379	I234N	probably benign	Het
Actrt3	A	G	3: 30,599,698	V51A	probably damaging	Het
Adgb	C	T	10: 10,431,281		probably null	Het
AI481877	A	C	4: 59,093,850	L226R	probably damaging	Het
Als2	A	G	1: 59,211,137	S483P	probably damaging	Het
Ankrd10	C	T	8: 11,615,682	R306H	probably damaging	Het
Arhgef10	T	C	8: 14,975,093		probably null	Het
Arhgef10	A	G	8: 14,975,666	I459V	probably benign	Het
Armc2	C	T	10: 41,966,700		probably null	Het
Atp12a	A	G	14: 56,386,950	R952G	possibly damaging	Het
Atp6v1g1	A	G	4: 63,550,021	Y87C	probably benign	Het
C030034I22Rik	T	A	17: 69,418,111		noncoding transcript	Het
Cacna2d1	G	A	5: 16,312,568	C404Y	probably damaging	Het
Ccdc163	T	C	4: 116,741,861		silent	Het
Ccdc59	A	T	10: 105,841,527	K9M	possibly damaging	Het
Clasrp	C	A	7: 19,585,240		probably benign	Het
Csmd2	T	C	4: 128,557,718	F113S	unknown	Het
Csmd3	C	T	15: 47,857,924	G1437D	probably damaging	Het
Cyp4a14	C	A	4: 115,487,301	G456W	probably damaging	Het
Cyp4a30b	A	G	4: 115,458,362	H260R	possibly damaging	Het
Dcp1b	C	T	6: 119,214,774	S217L	probably benign	Het
Dhx57	A	T	17: 80,251,376	D1051E	probably benign	Het
Dmp1	A	G	5: 104,212,108	S217G	probably benign	Het
Eif4enif1	C	T	11: 3,242,586	P805S	probably damaging	Het
Eral1	A	G	11: 78,076,278	I164T	possibly damaging	Het
Esr1	G	A	10: 4,997,890	R481H	probably damaging	Het
Fam19a2	A	T	10: 123,704,365	H42L	possibly damaging	Het
Fan1	A	G	7: 64,363,190	I668T	probably benign	Het
Gbp11	C	T	5: 105,331,000	D191N	probably benign	Het
Gm21759	T	A	5: 8,180,863		probably benign	Het
Gm5454	C	A	13: 103,357,523		noncoding transcript	Het
Gm9874	A	T	17: 30,485,789		probably benign	Het
Gria2	G	A	3: 80,702,492	T670I	probably damaging	Het
Gria4	T	A	9: 4,503,614	N334I	probably damaging	Het
Grm5	T	C	7: 87,602,722	V60A	possibly damaging	Het
Ift172	C	T	5: 31,257,861	V1335I	probably benign	Het
Ino80d	C	T	1: 63,061,039		probably null	Het
Kif1c	A	G	11: 70,724,081	E567G	probably damaging	Het
Krt31	T	G	11: 100,047,873	N298T	possibly damaging	Het
Mapk7	C	A	11: 61,490,212		probably benign	Het
March8	C	T	6: 116,401,145		probably benign	Het
Matr3	T	A	18: 35,572,296	S91R	probably benign	Het
Mdm1	A	G	10: 118,150,942	T267A	probably benign	Het
Mlxip	A	G	5: 123,452,667	M878V	probably benign	Het
Mtm1	T	C	X: 71,296,362		probably benign	Homo
Mtor	T	A	4: 148,540,030	M2089K	probably benign	Het
Mylk2	A	G	2: 152,919,348	K457R	probably damaging	Het
Nell1	A	T	7: 50,249,657		probably benign	Het
Nomo1	C	A	7: 46,046,937	T293N	probably damaging	Het
Odf3l2	G	A	10: 79,645,653	T14I	probably benign	Het
Olfr1080	T	C	2: 86,553,584	D180G	possibly damaging	Het
Olfr1510	T	G	14: 52,410,861	T4P	probably benign	Het
Olfr801	A	T	10: 129,669,759	C253*	probably null	Het
Ostc	T	C	3: 130,703,508	N80S	probably damaging	Het
Otud4	T	A	8: 79,661,073	N300K	possibly damaging	Het
Otx1	A	G	11: 21,998,681		probably benign	Het
Palmd	T	C	3: 116,923,751	R366G	possibly damaging	Het
Pcdhb20	A	T	18: 37,505,780	Q453L	possibly damaging	Het
Pcdhga9	T	A	18: 37,737,471	Y118N	possibly damaging	Het
Pes1	C	A	11: 3,976,834	T372K	probably benign	Het
Plcl1	A	T	1: 55,697,150	D550V	probably benign	Het
Plekhg5	T	A	4: 152,107,503	C433S	probably benign	Het
Plin2	A	G	4: 86,668,678	M1T	probably null	Het
Pold1	C	T	7: 44,543,347		silent	Het
Ppp1r7	T	A	1: 93,357,863		probably null	Het
Psmb8	T	C	17: 34,200,170	I146T	probably damaging	Het
Pzp	A	T	6: 128,485,556		probably null	Het
Rel	T	C	11: 23,761,129	I13V	probably benign	Het
Reln	C	T	5: 22,049,791	V527I	possibly damaging	Het
Retnla	A	G	16: 48,843,612	R90G	probably benign	Het
Slc39a8	T	A	3: 135,886,793		probably null	Het
Slc5a8	A	G	10: 88,904,963	I247V	probably benign	Het
Son	A	G	16: 91,664,317		probably null	Het
Spcs2	T	C	7: 99,839,761	D240G	probably damaging	Het
St5	A	T	7: 109,557,430	Y38N	probably benign	Het
Stx3	A	T	19: 11,789,574	V91D	probably damaging	Het
Taf6l	A	G	19: 8,778,628		probably benign	Het
Tbc1d8	A	G	1: 39,405,317	F187S	probably damaging	Het
Thbs1	C	G	2: 118,119,378	N611K	probably damaging	Het
Tipin	A	C	9: 64,304,327	S232R	probably benign	Het
Tmem132b	A	G	5: 125,638,268	D347G	probably benign	Het
Tmem161a	C	T	8: 70,178,915		probably benign	Het
Vmn2r68	A	C	7: 85,233,626	M306R	probably benign	Het
Vwa7	G	A	17: 35,021,242	M395I	probably damaging	Het
Ybx3	G	A	6: 131,370,413	A253V	probably damaging	Het
Zfp53	A	T	17: 21,508,078	E124D	probably benign	Het
Zzz3	T	A	3: 152,446,844		silent	Het

Other mutations in Cd6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00823:Cd6	APN	19	10796394	splice site	probably benign
IGL01326:Cd6	APN	19	10791102	missense	probably benign	0.09
IGL01406:Cd6	APN	19	10791137	missense	possibly damaging	0.77
IGL01885:Cd6	APN	19	10799237	missense	probably benign
IGL02268:Cd6	APN	19	10796388	missense	probably benign	0.03
IGL03100:Cd6	APN	19	10792939	missense	probably benign	0.34
Chapel	UTSW	19	10799491	missense	probably benign
digression	UTSW	19	10798358	nonsense	probably null
R1856:Cd6	UTSW	19	10798602	missense	probably damaging	0.98
R2419:Cd6	UTSW	19	10792852	missense	probably damaging	1.00
R2869:Cd6	UTSW	19	10794626	missense	possibly damaging	0.86
R2869:Cd6	UTSW	19	10794626	missense	possibly damaging	0.86
R2870:Cd6	UTSW	19	10794626	missense	possibly damaging	0.86
R2874:Cd6	UTSW	19	10794626	missense	possibly damaging	0.86
R2936:Cd6	UTSW	19	10796322	splice site	probably null
R4124:Cd6	UTSW	19	10790608	missense	probably damaging	1.00
R4748:Cd6	UTSW	19	10794225	nonsense	probably null
R6665:Cd6	UTSW	19	10791003	missense	probably benign	0.03
R6720:Cd6	UTSW	19	10794609	missense	probably benign	0.09
R7793:Cd6	UTSW	19	10798358	nonsense	probably null
R8122:Cd6	UTSW	19	10792867	missense	probably damaging	1.00
R8998:Cd6	UTSW	19	10799278	missense	probably damaging	1.00
R8999:Cd6	UTSW	19	10799278	missense	probably damaging	1.00
R9147:Cd6	UTSW	19	10799491	missense	probably benign
R9148:Cd6	UTSW	19	10799491	missense	probably benign
R9735:Cd6	UTSW	19	10797871	missense	probably benign	0.00
Z1177:Cd6	UTSW	19	10791445	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GGGCATGCTGGGAAAATCTTTC -3'
(R):5'- AAGTGGATCAGTTCATGGGTAG -3'

Sequencing Primer
(F):5'- TCCCACCATCAAGAGGTTTGG -3'
(R):5'- TGGATCAGTTCATGGGTAGAAAGTC -3'

Posted On

2015-02-18