Mutagenetix > Incidental Mutation

Incidental Mutation 'R5642:Cd44'

440716

Institutional Source

Beutler Lab

Gene Symbol

Cd44

Ensembl Gene

ENSMUSG00000005087

Gene Name

CD44 antigen

Synonyms

Pgp-1, Ly-24, HERMES

MMRRC Submission

043290-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.238) question?

Stock #

R5642 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

102641486-102732010 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 102731687 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 2 (D2G)

Ref Sequence

ENSEMBL: ENSMUSP00000106825 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000005218] [ENSMUST00000060516] [ENSMUST00000099673] [ENSMUST00000111190] [ENSMUST00000111191] [ENSMUST00000111192] [ENSMUST00000111194] [ENSMUST00000111198]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000005218
AA Change: D2G

PolyPhen 2 Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000005218
Gene: ENSMUSG00000005087
AA Change: D2G

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
LINK	34	125	5.88e-38	SMART
low complexity region	251	276	N/A	INTRINSIC
low complexity region	429	439	N/A	INTRINSIC
low complexity region	640	653	N/A	INTRINSIC
low complexity region	689	703	N/A	INTRINSIC
PDB:2ZPY\|B	710	729	1e-6	PDB

Predicted Effect

possibly damaging
Transcript: ENSMUST00000060516
AA Change: D2G

PolyPhen 2 Score 0.475 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000062330
Gene: ENSMUSG00000005087
AA Change: D2G

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
LINK	34	125	5.88e-38	SMART
low complexity region	229	239	N/A	INTRINSIC
low complexity region	440	453	N/A	INTRINSIC
low complexity region	489	503	N/A	INTRINSIC
PDB:2ZPY\|B	510	529	1e-6	PDB

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000083749

Predicted Effect

possibly damaging
Transcript: ENSMUST00000099673
AA Change: D2G

PolyPhen 2 Score 0.798 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000097265
Gene: ENSMUSG00000005087
AA Change: D2G

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
LINK	34	125	5.88e-38	SMART
low complexity region	225	238	N/A	INTRINSIC
low complexity region	274	288	N/A	INTRINSIC
PDB:2ZPY\|B	295	314	1e-6	PDB

Predicted Effect

probably damaging
Transcript: ENSMUST00000111190
AA Change: D2G

PolyPhen 2 Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000106821
Gene: ENSMUSG00000005087
AA Change: D2G

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
LINK	34	125	5.88e-38	SMART
low complexity region	324	337	N/A	INTRINSIC
low complexity region	373	387	N/A	INTRINSIC
PDB:2ZPY\|B	394	413	8e-7	PDB

Predicted Effect

possibly damaging
Transcript: ENSMUST00000111191
AA Change: D2G

PolyPhen 2 Score 0.911 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000106822
Gene: ENSMUSG00000005087
AA Change: D2G

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
LINK	34	125	5.88e-38	SMART
low complexity region	358	371	N/A	INTRINSIC
low complexity region	407	421	N/A	INTRINSIC
PDB:2ZPY\|B	428	447	9e-7	PDB

Predicted Effect

probably damaging
Transcript: ENSMUST00000111192
AA Change: D2G

PolyPhen 2 Score 0.958 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000106823
Gene: ENSMUSG00000005087
AA Change: D2G

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
LINK	34	125	5.88e-38	SMART
low complexity region	294	307	N/A	INTRINSIC
low complexity region	343	357	N/A	INTRINSIC
PDB:2ZPY\|B	364	383	1e-6	PDB

Predicted Effect

probably damaging
Transcript: ENSMUST00000111194
AA Change: D2G

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000106825
Gene: ENSMUSG00000005087
AA Change: D2G

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
LINK	34	125	5.88e-38	SMART
low complexity region	268	278	N/A	INTRINSIC
low complexity region	302	312	N/A	INTRINSIC
low complexity region	437	450	N/A	INTRINSIC
low complexity region	486	500	N/A	INTRINSIC
PDB:2ZPY\|B	507	526	1e-6	PDB

Predicted Effect

probably damaging
Transcript: ENSMUST00000111198
AA Change: D2G

PolyPhen 2 Score 0.963 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000106829
Gene: ENSMUSG00000005087
AA Change: D2G

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
LINK	34	125	5.88e-38	SMART
low complexity region	306	316	N/A	INTRINSIC
low complexity region	517	530	N/A	INTRINSIC
low complexity region	566	580	N/A	INTRINSIC
PDB:2ZPY\|B	587	606	1e-6	PDB

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000124624

Meta Mutation Damage Score

0.2048

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.1%
20x: 94.8%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a cell-surface glycoprotein involved in cell-cell interactions, cell adhesion and migration. It is a receptor for hyaluronic acid (HA) and can also interact with other ligands, such as osteopontin, collagens, and matrix metalloproteinases (MMPs). This protein participates in a wide variety of cellular functions including lymphocyte activation, recirculation and homing, hematopoiesis, and tumor metastasis. Transcripts for this gene undergo complex alternative splicing that results in many functionally distinct isoforms, however, the full length nature of some of these variants has not been determined. Alternative splicing is the basis for the structural and functional diversity of this protein, and may be related to tumor metastasis. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted null mutations exhibit impaired T lymphocyte trafficking resulting in muted inflammatory responses, altered myeloid progenitor distribution, reduced growth of tumors, and impaired uterine involution and maintenance of lactation. [provided by MGI curators]

Allele List at MGI

All alleles(7) : Targeted, knock-out(4) Targeted, other(3)

Other mutations in this stock

Total: 93 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc1	A	G	16: 14,261,319 (GRCm39)	E699G	probably damaging	Het
Ap4e1	T	A	2: 126,906,899 (GRCm39)	V1053D	possibly damaging	Het
Apobec1	T	A	6: 122,558,456 (GRCm39)	I100F	probably damaging	Het
Atp6v1g3	G	T	1: 138,211,480 (GRCm39)	K53N	probably damaging	Het
Bag3	C	T	7: 128,147,830 (GRCm39)	R482W	probably damaging	Het
Brme1	C	T	8: 84,894,114 (GRCm39)	T427I	probably damaging	Het
Cacna1i	A	G	15: 80,279,279 (GRCm39)	T2007A	possibly damaging	Het
Cdadc1	T	A	14: 59,827,372 (GRCm39)	I100F	possibly damaging	Het
Cdh16	A	G	8: 105,344,677 (GRCm39)	F485L	probably damaging	Het
Cdhr5	T	A	7: 140,849,110 (GRCm39)	K817*	probably null	Het
Cfap46	G	T	7: 139,258,493 (GRCm39)	P260Q	probably damaging	Het
Clec11a	C	T	7: 43,955,832 (GRCm39)	E72K	possibly damaging	Het
Cnr2	C	A	4: 135,644,076 (GRCm39)	N51K	probably damaging	Het
Col3a1	T	A	1: 45,370,872 (GRCm39)		probably benign	Het
Cxcr1	G	A	1: 74,230,987 (GRCm39)	T345M	probably damaging	Het
Cyp2s1	T	C	7: 25,515,744 (GRCm39)		probably null	Het
Dalrd3	C	T	9: 108,449,489 (GRCm39)	T474M	probably damaging	Het
Ddit4	C	T	10: 59,787,327 (GRCm39)	S3N	probably benign	Het
Ddx41	T	C	13: 55,683,708 (GRCm39)	K108E	possibly damaging	Het
Dnaaf10	A	G	11: 17,177,263 (GRCm39)	N207S	possibly damaging	Het
Ece2	A	T	16: 20,462,477 (GRCm39)	H732L	probably benign	Het
Etv3	T	G	3: 87,443,322 (GRCm39)	L302R	possibly damaging	Het
Fam135b	A	G	15: 71,333,985 (GRCm39)	S1070P	probably damaging	Het
Fhip1b	A	T	7: 105,039,089 (GRCm39)	I50N	probably damaging	Het
Gm11567	T	A	11: 99,770,437 (GRCm39)	I125N	unknown	Het
Grm3	A	G	5: 9,620,536 (GRCm39)	L236P	probably benign	Het
Hip1	T	A	5: 135,461,939 (GRCm39)	R97*	probably null	Het
Hoxa5	T	C	6: 52,181,197 (GRCm39)	Y45C	probably damaging	Het
Ighg1	T	A	12: 113,292,654 (GRCm39)	H305L	probably damaging	Het
Inpp5b	T	A	4: 124,676,229 (GRCm39)	C362S	probably benign	Het
Kif1c	A	G	11: 70,599,273 (GRCm39)	K391E	probably benign	Het
Klf9	T	C	19: 23,119,246 (GRCm39)	V43A	probably benign	Het
Krt28	T	A	11: 99,265,320 (GRCm39)	I116F	probably damaging	Het
Lct	A	T	1: 128,222,969 (GRCm39)	D1439E	probably damaging	Het
Liph	G	A	16: 21,784,745 (GRCm39)	T284M	possibly damaging	Het
Lrrc75b	T	C	10: 75,393,055 (GRCm39)	K98R	possibly damaging	Het
Lypd4	T	C	7: 24,564,604 (GRCm39)	Q178R	probably benign	Het
Map1a	T	A	2: 121,136,524 (GRCm39)	S2209T	probably damaging	Het
Map3k21	C	T	8: 126,665,563 (GRCm39)	T584I	probably benign	Het
Map3k6	T	C	4: 132,972,855 (GRCm39)	V338A	probably damaging	Het
Mapk8ip3	A	T	17: 25,122,285 (GRCm39)	V699E	possibly damaging	Het
Mtarc1	A	C	1: 184,543,116 (GRCm39)	S71A	probably damaging	Het
Nckap1l	T	C	15: 103,363,452 (GRCm39)	S53P	probably benign	Het
Nt5e	T	C	9: 88,209,740 (GRCm39)	M1T	probably null	Het
Nudt22	T	C	19: 6,972,896 (GRCm39)	H64R	probably damaging	Het
Or1o11	A	T	17: 37,756,663 (GRCm39)	T84S	probably damaging	Het
Or2t44	A	T	11: 58,677,654 (GRCm39)	Y198F	probably damaging	Het
Or2w3	T	C	11: 58,557,225 (GRCm39)	I280T	possibly damaging	Het
Or52b1	A	T	7: 104,978,772 (GRCm39)	V209D	probably damaging	Het
Or5ac16	A	G	16: 59,022,369 (GRCm39)	L140P	probably damaging	Het
Or8k17	T	C	2: 86,066,276 (GRCm39)	N294S	probably damaging	Het
Otogl	T	C	10: 107,722,413 (GRCm39)	I314V	probably benign	Het
Pan2	G	T	10: 128,143,969 (GRCm39)	E106D	probably benign	Het
Papss1	T	A	3: 131,337,565 (GRCm39)	Y554*	probably null	Het
Pcnx1	T	C	12: 81,941,803 (GRCm39)	V67A	possibly damaging	Het
Pdpk1	A	C	17: 24,325,829 (GRCm39)	Y122*	probably null	Het
Pkd1l1	A	T	11: 8,829,202 (GRCm39)	N1463K	probably damaging	Het
Ptgfrn	C	A	3: 100,950,678 (GRCm39)	M878I	probably damaging	Het
Ranbp3	G	A	17: 57,017,703 (GRCm39)	G453E	probably benign	Het
Rapgef2	T	C	3: 79,002,157 (GRCm39)	D261G	probably damaging	Het
Reep2	A	G	18: 34,979,271 (GRCm39)	S199G	probably benign	Het
Rnpep	G	A	1: 135,205,259 (GRCm39)	T202I	probably damaging	Het
Sass6	T	A	3: 116,401,145 (GRCm39)		probably null	Het
Sema3e	A	G	5: 14,212,257 (GRCm39)	D111G	probably damaging	Het
Slc29a4	A	G	5: 142,697,727 (GRCm39)	E60G	probably damaging	Het
Spata31g1	T	C	4: 42,971,831 (GRCm39)	L388P	possibly damaging	Het
Spata31h1	T	A	10: 82,120,317 (GRCm39)	Q4231L	probably damaging	Het
Sptlc3	T	C	2: 139,388,328 (GRCm39)	Y107H	probably damaging	Het
Stx6	T	C	1: 155,073,925 (GRCm39)	I245T	probably benign	Het
Syne2	T	C	12: 75,965,306 (GRCm39)	S774P	probably damaging	Het
Tbc1d16	T	A	11: 119,049,617 (GRCm39)	Q293L	probably damaging	Het
Tbc1d30	T	C	10: 121,132,692 (GRCm39)	D224G	probably damaging	Het
Tbc1d32	T	A	10: 56,026,973 (GRCm39)	N759Y	possibly damaging	Het
Tdrd12	G	T	7: 35,210,725 (GRCm39)	A166E	probably damaging	Het
Tex14	A	G	11: 87,405,046 (GRCm39)	R653G	probably benign	Het
Them6	A	T	15: 74,593,654 (GRCm39)	R171W	probably null	Het
Tln2	T	C	9: 67,203,640 (GRCm39)	T489A	probably benign	Het
Tmem87a	A	G	2: 120,234,427 (GRCm39)	F39L	probably benign	Het
Toporsl	T	A	4: 52,611,515 (GRCm39)	C469*	probably null	Het
Tpr	T	C	1: 150,299,569 (GRCm39)	S1147P	probably damaging	Het
Trp53bp1	T	C	2: 121,067,143 (GRCm39)	M528V	probably benign	Het
Trpm6	T	A	19: 18,807,571 (GRCm39)	C1039S	probably damaging	Het
Ttc16	T	A	2: 32,665,348 (GRCm39)	S5C	probably damaging	Het
Ttn	T	C	2: 76,617,412 (GRCm39)	Y14607C	probably damaging	Het
Usp6nl	T	C	2: 6,435,275 (GRCm39)	F345L	probably damaging	Het
Vmn1r205	C	T	13: 22,776,206 (GRCm39)	G299R	probably benign	Het
Vmn2r74	G	A	7: 85,606,588 (GRCm39)	H253Y	probably benign	Het
Vps13d	A	T	4: 144,896,872 (GRCm39)	D343E	possibly damaging	Het
Vwf	A	G	6: 125,580,381 (GRCm39)	E543G		Het
Zfat	A	T	15: 68,052,765 (GRCm39)	V343E	probably damaging	Het
Zfp316	T	C	5: 143,249,846 (GRCm39)	E139G	unknown	Het
Zfp943	T	A	17: 22,211,813 (GRCm39)	C300S	probably damaging	Het
Zkscan16	A	G	4: 58,957,748 (GRCm39)	K677E	probably benign	Het

Other mutations in Cd44

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00543:Cd44	APN	2	102,686,292 (GRCm39)	missense	possibly damaging	0.73
IGL01087:Cd44	APN	2	102,652,607 (GRCm39)	missense	probably damaging	1.00
IGL01413:Cd44	APN	2	102,644,632 (GRCm39)	missense	probably damaging	0.99
IGL01830:Cd44	APN	2	102,672,603 (GRCm39)	splice site	probably benign
IGL02221:Cd44	APN	2	102,676,858 (GRCm39)	missense	probably benign	0.01
IGL02271:Cd44	APN	2	102,661,732 (GRCm39)	missense	possibly damaging	0.93
IGL02552:Cd44	APN	2	102,679,076 (GRCm39)	missense	probably benign	0.01
IGL02861:Cd44	APN	2	102,662,826 (GRCm39)	critical splice donor site	probably null
IGL03309:Cd44	APN	2	102,644,522 (GRCm39)	missense	probably damaging	1.00
IGL03352:Cd44	APN	2	102,675,759 (GRCm39)	intron	probably benign
Jialin	UTSW	2	102,695,715 (GRCm39)	missense	probably damaging	0.99
Kale	UTSW	2	102,654,648 (GRCm39)	missense	probably damaging	0.99
N/A - 535:Cd44	UTSW	2	102,644,534 (GRCm39)	missense	possibly damaging	0.50
R0488:Cd44	UTSW	2	102,664,564 (GRCm39)	splice site	probably benign
R1441:Cd44	UTSW	2	102,676,763 (GRCm39)	missense	probably damaging	0.99
R1482:Cd44	UTSW	2	102,661,728 (GRCm39)	missense	probably damaging	1.00
R1497:Cd44	UTSW	2	102,673,300 (GRCm39)	splice site	probably null
R1803:Cd44	UTSW	2	102,664,597 (GRCm39)	missense	probably damaging	1.00
R1952:Cd44	UTSW	2	102,683,432 (GRCm39)	missense	probably damaging	0.98
R2093:Cd44	UTSW	2	102,644,629 (GRCm39)	missense	probably damaging	1.00
R2180:Cd44	UTSW	2	102,658,955 (GRCm39)	missense	possibly damaging	0.66
R2425:Cd44	UTSW	2	102,691,931 (GRCm39)	missense	probably damaging	1.00
R3687:Cd44	UTSW	2	102,731,695 (GRCm39)	splice site	probably null
R3820:Cd44	UTSW	2	102,731,738 (GRCm39)	splice site	probably null
R3821:Cd44	UTSW	2	102,731,738 (GRCm39)	splice site	probably null
R3822:Cd44	UTSW	2	102,731,738 (GRCm39)	splice site	probably null
R4060:Cd44	UTSW	2	102,731,687 (GRCm39)	missense	probably damaging	1.00
R4633:Cd44	UTSW	2	102,683,392 (GRCm39)	missense	possibly damaging	0.86
R4647:Cd44	UTSW	2	102,668,274 (GRCm39)	missense	possibly damaging	0.68
R4780:Cd44	UTSW	2	102,691,910 (GRCm39)	missense	probably damaging	1.00
R5087:Cd44	UTSW	2	102,661,699 (GRCm39)	missense	possibly damaging	0.83
R5118:Cd44	UTSW	2	102,695,715 (GRCm39)	missense	probably damaging	0.99
R5449:Cd44	UTSW	2	102,662,891 (GRCm39)	missense	probably damaging	1.00
R5928:Cd44	UTSW	2	102,654,648 (GRCm39)	missense	probably damaging	0.99
R5995:Cd44	UTSW	2	102,692,015 (GRCm39)	missense	probably damaging	1.00
R5999:Cd44	UTSW	2	102,675,742 (GRCm39)	missense	probably benign	0.42
R7050:Cd44	UTSW	2	102,644,482 (GRCm39)	missense	probably damaging	0.99
R7350:Cd44	UTSW	2	102,664,607 (GRCm39)	missense	probably benign	0.19
R7797:Cd44	UTSW	2	102,679,079 (GRCm39)	missense	probably benign	0.34
R7866:Cd44	UTSW	2	102,672,604 (GRCm39)	critical splice donor site	probably null
R8138:Cd44	UTSW	2	102,662,842 (GRCm39)	missense	probably benign	0.00
R8185:Cd44	UTSW	2	102,654,665 (GRCm39)	missense	possibly damaging	0.52
R8732:Cd44	UTSW	2	102,664,645 (GRCm39)	missense	possibly damaging	0.67
R8955:Cd44	UTSW	2	102,683,363 (GRCm39)	missense	probably damaging	0.98
R9249:Cd44	UTSW	2	102,661,747 (GRCm39)	missense	possibly damaging	0.51
R9548:Cd44	UTSW	2	102,661,832 (GRCm39)	missense	possibly damaging	0.58

Predicted Primers

PCR Primer
(F):5'- GCTTTGCTAGCCCAATTCAC -3'
(R):5'- TTGGCTGCTTAGTCACAGC -3'

Sequencing Primer
(F):5'- TTGCTAGCCCAATTCACTACAG -3'
(R):5'- TAGTCACAGCCCCCTCG -3'

Posted On

2016-11-08