Mutagenetix > Incidental Mutation

Incidental Mutation 'R6273:Cd1d1'

507441

Institutional Source

Beutler Lab

Gene Symbol

Cd1d1

Ensembl Gene

ENSMUSG00000028076

Gene Name

CD1d1 antigen

Synonyms

Cd1d, Cd1a, CD1.1, Ly-38

MMRRC Submission

044443-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.100) question?

Stock #

R6273 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

86903141-86906748 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 86905564 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 143 (V143A)

Ref Sequence

ENSEMBL: ENSMUSP00000029717 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029717] [ENSMUST00000063869]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000029717
AA Change: V143A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000029717
Gene: ENSMUSG00000028076
AA Change: V143A

Domain	Start	End	E-Value	Type
Pfam:MHC_I_3	1	200	1.3e-95	PFAM
IGc1	221	291	5.35e-22	SMART
transmembrane domain	304	326	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000063869

SMART Domains

Protein: ENSMUSP00000070616
Gene: ENSMUSG00000028076

Domain	Start	End	E-Value	Type
signal peptide	1	21	N/A	INTRINSIC
PDB:4MQ7\|A	23	73	2e-15	PDB
IGc1	90	160	5.35e-22	SMART
low complexity region	173	194	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000107620

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132131

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000142793

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.0%
20x: 94.2%

Validation Efficiency

98% (78/80)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a divergent member of the CD1 family of transmembrane glycoproteins, which are structurally related to the major histocompatibility complex (MHC) proteins and form heterodimers with beta-2-microglobulin. The CD1 proteins mediate the presentation of primarily lipid and glycolipid antigens of self or microbial origin to T cells. The human genome contains five CD1 family genes organized in a cluster on chromosome 1. The CD1 family members are thought to differ in their cellular localization and specificity for particular lipid ligands. The protein encoded by this gene localizes to late endosomes and lysosomes via a tyrosine-based motif in the cytoplasmic tail. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]
PHENOTYPE: Homozygotes for targeted null mutations lack natural killer T cells, and mutant splenocytes fail to produce interleukin 4 (IL4). [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610040J01Rik	T	A	5: 64,055,561 (GRCm39)	I99N	probably damaging	Het
Ank3	G	A	10: 69,838,395 (GRCm39)	R1566K	possibly damaging	Het
Ankrd31	A	G	13: 96,988,181 (GRCm39)	I1065V	possibly damaging	Het
Aox1	A	G	1: 58,378,831 (GRCm39)	T1027A	probably benign	Het
Atm	G	A	9: 53,399,222 (GRCm39)	P1593L	probably benign	Het
Atp13a5	T	G	16: 29,167,555 (GRCm39)	I132L	probably benign	Het
BC035044	A	G	6: 128,867,852 (GRCm39)		probably benign	Het
Cadm3	CT	C	1: 173,176,691 (GRCm39)		probably benign	Homo
Car3	C	T	3: 14,936,677 (GRCm39)	P247S	probably benign	Het
Ccdc7a	T	C	8: 129,513,819 (GRCm39)	Y160C	probably damaging	Het
Cemip2	T	A	19: 21,779,369 (GRCm39)	V393E	probably damaging	Het
Cog6	A	T	3: 52,903,473 (GRCm39)	F142I	probably damaging	Het
Cracd	A	T	5: 77,005,568 (GRCm39)	D643V	unknown	Het
Crhr1	T	G	11: 104,054,682 (GRCm39)	N98K	possibly damaging	Het
Csf1	A	G	3: 107,656,479 (GRCm39)	V72A	probably damaging	Het
Cwc15	T	A	9: 14,421,537 (GRCm39)	I201K	probably benign	Het
Dgka	T	C	10: 128,559,515 (GRCm39)	K482R	probably benign	Het
Dnah7b	T	C	1: 46,281,476 (GRCm39)	S2846P	possibly damaging	Het
Dst	T	A	1: 34,314,347 (GRCm39)	I4199N	probably damaging	Het
Dusp7	A	G	9: 106,251,095 (GRCm39)	T407A	possibly damaging	Het
Eml2	G	A	7: 18,935,088 (GRCm39)	V432I	probably damaging	Het
Fem1a	T	C	17: 56,564,083 (GRCm39)	Y59H	possibly damaging	Het
Fetub	C	T	16: 22,751,081 (GRCm39)	R143C	probably damaging	Het
Filip1	A	T	9: 79,723,168 (GRCm39)	D1150E	probably benign	Het
Gabra1	A	G	11: 42,031,138 (GRCm39)	V264A	probably damaging	Het
Gm4131	T	C	14: 62,702,299 (GRCm39)	E223G	probably damaging	Het
Gon4l	T	C	3: 88,763,156 (GRCm39)	V333A	probably damaging	Het
Gsk3b	A	G	16: 38,028,408 (GRCm39)	T289A	probably benign	Het
Hmcn2	T	C	2: 31,301,846 (GRCm39)	S2912P	probably damaging	Het
Htr7	A	T	19: 36,018,969 (GRCm39)		probably benign	Het
Ibsp	A	G	5: 104,458,167 (GRCm39)	T235A	probably benign	Het
Ints13	A	T	6: 146,467,179 (GRCm39)	D116E	probably damaging	Het
Irag1	G	T	7: 110,470,790 (GRCm39)	H848N	probably benign	Het
Kctd19	T	C	8: 106,112,117 (GRCm39)	N753S	probably benign	Het
Mdn1	A	G	4: 32,715,979 (GRCm39)	N2054D	probably benign	Het
Mink1	A	T	11: 70,502,261 (GRCm39)	K880*	probably null	Het
Myo15b	T	A	11: 115,753,625 (GRCm39)	L824Q	possibly damaging	Het
Napepld	T	C	5: 21,870,320 (GRCm39)	E366G	probably benign	Het
Obscn	T	A	11: 58,967,819 (GRCm39)	T2662S	possibly damaging	Het
Or2g7	T	G	17: 38,378,686 (GRCm39)	L208R	probably damaging	Het
Or2n1b	T	A	17: 38,459,833 (GRCm39)	M118K	possibly damaging	Het
Or4k52	T	C	2: 111,611,567 (GRCm39)	F301L	probably benign	Het
Or52p1	A	G	7: 104,267,102 (GRCm39)	D72G	probably damaging	Het
Or5b12	A	G	19: 12,896,764 (GRCm39)	V303A	probably benign	Het
Or6d13	A	G	6: 116,518,277 (GRCm39)	T288A	possibly damaging	Het
Pah	T	C	10: 87,412,077 (GRCm39)		probably null	Het
Panx3	T	G	9: 37,578,725 (GRCm39)	I85L	probably benign	Het
Pate4	T	C	9: 35,519,086 (GRCm39)	N94D	probably benign	Het
Pde4d	A	G	13: 110,086,755 (GRCm39)	M610V	possibly damaging	Het
Pik3c2b	T	C	1: 132,994,449 (GRCm39)	S138P	probably benign	Het
Pkn1	T	C	8: 84,398,899 (GRCm39)	N696S	probably damaging	Het
Plppr2	A	G	9: 21,855,801 (GRCm39)	E258G	probably damaging	Het
Plxnd1	A	T	6: 115,955,453 (GRCm39)	M538K	probably damaging	Het
Prepl	G	T	17: 85,390,696 (GRCm39)	N87K	probably benign	Het
Prkag2	C	A	5: 25,152,534 (GRCm39)	R190L	probably damaging	Het
Rara	A	G	11: 98,861,048 (GRCm39)	T179A	probably benign	Het
Rfx7	A	G	9: 72,524,279 (GRCm39)	K490E	possibly damaging	Het
Rgsl1	C	T	1: 153,703,211 (GRCm39)	V147M	possibly damaging	Het
Rph3a	A	G	5: 121,083,485 (GRCm39)	I595T	possibly damaging	Het
Rsf1	CG	CGACGGCGGTG	7: 97,229,115 (GRCm39)		probably benign	Homo
Slc35e2	C	T	4: 155,694,483 (GRCm39)	P10L	probably benign	Het
Slc8a2	T	C	7: 15,879,259 (GRCm39)	F582L	possibly damaging	Het
Sprr2e	A	G	3: 92,260,171 (GRCm39)	M1V	probably null	Het
Steap1	T	A	5: 5,790,827 (GRCm39)	R40S	possibly damaging	Het
Tbc1d2	C	T	4: 46,629,912 (GRCm39)	G252R	probably benign	Het
Thsd7a	A	T	6: 12,408,835 (GRCm39)	V729E	probably damaging	Het
Tmprss13	A	G	9: 45,256,630 (GRCm39)	Y525C	probably damaging	Het
Tnik	A	T	3: 28,631,649 (GRCm39)	H383L	possibly damaging	Het
Vars1	T	C	17: 35,232,719 (GRCm39)	L881S	probably damaging	Het
Vmn1r201	A	C	13: 22,659,385 (GRCm39)	S200R	probably damaging	Het
Vmn2r130	A	T	17: 23,295,759 (GRCm39)	H643L	probably benign	Het
Vmn2r14	A	T	5: 109,369,133 (GRCm39)	W147R	probably benign	Het
Vps53	T	C	11: 75,992,844 (GRCm39)	E367G	probably benign	Het
Xab2	C	T	8: 3,661,822 (GRCm39)	G544S	probably damaging	Het
Ythdf3	T	A	3: 16,259,020 (GRCm39)	V400E	possibly damaging	Het
Zfand5	C	T	19: 21,257,060 (GRCm39)	P147S	probably benign	Het
Zfp768	A	T	7: 126,944,319 (GRCm39)		probably null	Het
Zswim8	A	G	14: 20,763,521 (GRCm39)	M423V	probably benign	Het

Other mutations in Cd1d1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00588:Cd1d1	APN	3	86,905,480 (GRCm39)	missense	probably damaging	0.99
IGL01811:Cd1d1	APN	3	86,903,895 (GRCm39)	missense	possibly damaging	0.86
IGL02371:Cd1d1	APN	3	86,906,188 (GRCm39)	missense	probably benign	0.40
IGL03001:Cd1d1	APN	3	86,905,468 (GRCm39)	missense	probably benign
R0350:Cd1d1	UTSW	3	86,904,880 (GRCm39)	missense	probably benign	0.11
R1771:Cd1d1	UTSW	3	86,905,972 (GRCm39)	missense	possibly damaging	0.85
R2407:Cd1d1	UTSW	3	86,905,489 (GRCm39)	missense	probably damaging	1.00
R3906:Cd1d1	UTSW	3	86,906,063 (GRCm39)	missense	probably damaging	1.00
R4540:Cd1d1	UTSW	3	86,904,012 (GRCm39)	missense	probably benign	0.21
R4976:Cd1d1	UTSW	3	86,905,958 (GRCm39)	missense	probably benign	0.00
R5303:Cd1d1	UTSW	3	86,905,427 (GRCm39)	missense	probably benign	0.22
R5786:Cd1d1	UTSW	3	86,906,095 (GRCm39)	missense	probably benign	0.17
R6088:Cd1d1	UTSW	3	86,906,009 (GRCm39)	missense	probably benign	0.07
R7315:Cd1d1	UTSW	3	86,905,420 (GRCm39)	missense	possibly damaging	0.80
R7787:Cd1d1	UTSW	3	86,904,903 (GRCm39)	missense	probably damaging	0.98
R8854:Cd1d1	UTSW	3	86,905,480 (GRCm39)	missense	probably damaging	0.99
R8957:Cd1d1	UTSW	3	86,906,140 (GRCm39)	missense	probably damaging	0.99
R9079:Cd1d1	UTSW	3	86,906,197 (GRCm39)	missense	probably benign
R9328:Cd1d1	UTSW	3	86,905,459 (GRCm39)	missense	possibly damaging	0.80
R9368:Cd1d1	UTSW	3	86,905,939 (GRCm39)	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- GGTGAAAATAGCCAGCTGACC -3'
(R):5'- ATTTTCCTCAACTGGCACTTAACG -3'

Sequencing Primer
(F):5'- GAAAATAGCCAGCTGACCTTGCTTC -3'
(R):5'- CAACTGGCACTTAACGATAATCTTC -3'

Posted On

2018-03-15