Mutagenetix > Incidental Mutations

Incidental Mutation 'R6720:Cd6'

529565

Institutional Source

Beutler Lab

Gene Symbol

Cd6

Ensembl Gene

ENSMUSG00000024670

Gene Name

CD6 antigen

Synonyms

MMRRC Submission

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.063) question?

Stock #

R6720 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

10789341-10830058 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 10794609 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Serine at position 414 (T414S)

Ref Sequence

ENSEMBL: ENSMUSP00000079172 (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: T414S

PolyPhen 2 Score 0.091 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000046861
Gene: ENSMUSG00000024670
AA Change: T414S

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: T414S

PolyPhen 2 Score 0.091 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000079172
Gene: ENSMUSG00000024670
AA Change: T414S

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

probably benign
Transcript: ENSMUST00000174176
AA Change: T313S

PolyPhen 2 Score 0.035 (Sensitivity: 0.94; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000134639
Gene: ENSMUSG00000024670
AA Change: T313S

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

0.0898

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.7%
20x: 93.6%

Validation Efficiency

98% (50/51)

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: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700013G24Rik	G	A	4: 137,454,686	E51K	possibly damaging	Het
Abca1	A	C	4: 53,083,733	L700R	probably damaging	Het
Arpc1a	C	A	5: 145,101,222		probably null	Het
Baz2b	G	T	2: 59,924,890	P241Q	probably damaging	Het
Ces2b	A	T	8: 104,836,869	E409D	probably benign	Het
Cfap54	A	G	10: 92,821,119	Y3024H	probably benign	Het
Chrm1	A	G	19: 8,678,548	T206A	probably benign	Het
Clptm1l	T	C	13: 73,618,516	W512R	probably damaging	Het
Col15a1	T	A	4: 47,247,552		probably null	Het
Cox15	A	G	19: 43,736,789	S392P	probably damaging	Het
Cr2	T	C	1: 195,155,200	M1197V	probably damaging	Het
Ddx60	A	G	8: 62,000,689	K1281E	probably benign	Het
Dnah11	A	G	12: 118,045,646	F2094L	probably damaging	Het
Ear2	T	A	14: 44,102,959	C25S	probably damaging	Het
Ect2l	T	C	10: 18,140,264	D802G	probably damaging	Het
Eftud2	G	A	11: 102,838,623	Q84*	probably null	Het
Eif4g3	T	A	4: 138,175,832		probably null	Het
Ephb2	T	C	4: 136,657,502	D866G	probably damaging	Het
Fam129b	T	A	2: 32,905,826	V22D	probably damaging	Het
Farsb	A	G	1: 78,472,497	M99T	probably damaging	Het
Foxs1	T	A	2: 152,932,720	S138C	probably damaging	Het
Frem1	T	G	4: 83,013,832	S211R	probably damaging	Het
Gm19410	G	A	8: 35,807,576	R1517Q	probably benign	Het
Gria2	T	C	3: 80,802,304	I27M	probably benign	Het
H2-Q7	A	G	17: 35,442,678	E299G	probably benign	Het
Hao2	T	G	3: 98,877,135	I305L	probably benign	Het
Hectd4	C	T	5: 121,307,381	Q122*	probably null	Het
Hivep1	T	A	13: 42,164,284	C2079S	probably damaging	Het
Hoxb1	C	A	11: 96,366,987	Q248K	probably damaging	Het
Hspb6	A	G	7: 30,554,347	D95G	probably benign	Het
Ighv5-2	T	A	12: 113,578,506	R117S	probably damaging	Het
Ino80d	A	C	1: 63,058,610	S708R	probably damaging	Het
Lman1l	A	G	9: 57,614,072		probably null	Het
Mmp15	A	G	8: 95,365,314	N51D	probably benign	Het
Naip1	T	C	13: 100,423,077	M1140V	probably benign	Het
Olfr1053	A	G	2: 86,315,065	S74P	probably damaging	Het
Olfr1373	A	G	11: 52,144,693	V279A	probably benign	Het
Olfr397	A	G	11: 73,965,465	N286D	probably damaging	Het
Olfr890	T	A	9: 38,143,153	M1K	probably null	Het
Pard3b	A	T	1: 62,159,470	N239I	probably damaging	Het
Parvb	C	T	15: 84,297,979	R237W	probably damaging	Het
Pcdha9	T	C	18: 36,998,069	S64P	probably damaging	Het
Pdcd1	T	C	1: 94,041,389	N68S	probably benign	Het
Pi4ka	G	T	16: 17,326,052		probably null	Het
Plekha4	A	T	7: 45,540,886	D359V	possibly damaging	Het
Serpinb13	A	G	1: 106,994,062	I78V	probably benign	Het
Slc39a7	T	A	17: 34,030,108	T269S	probably benign	Het
Sltm	T	G	9: 70,573,710	D281E	probably damaging	Het
Zfp708	T	C	13: 67,071,432	Y76C	probably damaging	Het
Zfp990	T	A	4: 145,536,927	V165D	possibly damaging	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
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
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
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
Z1177:Cd6	UTSW	19	10791445	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ACTGGGCATGCTGGGAAAATC -3'
(R):5'- GGATCAGTTCATGGGTAGAAAGTC -3'

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

Posted On

2018-08-01