Mutagenetix > Incidental Mutation

Incidental Mutation 'R9762:Gpc6'

733103

Institutional Source

Beutler Lab

Gene Symbol

Gpc6

Ensembl Gene

ENSMUSG00000058571

Gene Name

glypican 6

Synonyms

6720429C22Rik

MMRRC Submission

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.139) question?

Stock #

R9762 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

117162727-118213956 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 118202258 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 489 (N489K)

Ref Sequence

ENSEMBL: ENSMUSP00000120362 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000078849] [ENSMUST00000088483] [ENSMUST00000125435]

AlphaFold

Q9R087

Predicted Effect

probably benign
Transcript: ENSMUST00000078849
AA Change: N479K

PolyPhen 2 Score 0.223 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000077893
Gene: ENSMUSG00000058571
AA Change: N479K

Domain	Start	End	E-Value	Type
Pfam:Glypican	7	554	9.3e-247	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000088483
AA Change: N479K

PolyPhen 2 Score 0.223 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000085835
Gene: ENSMUSG00000058571
AA Change: N479K

Domain	Start	End	E-Value	Type
Pfam:Glypican	7	554	9.3e-247	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000125435
AA Change: N489K

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000120362
Gene: ENSMUSG00000058571
AA Change: N489K

Domain	Start	End	E-Value	Type
Pfam:Glypican	15	564	7.2e-248	PFAM

Coding Region Coverage

1x: 99.9%
3x: 99.8%
10x: 99.4%
20x: 98.6%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The glypicans comprise a family of glycosylphosphatidylinositol-anchored heparan sulfate proteoglycans, and they have been implicated in the control of cell growth and cell division. The glypican encoded by this gene is a putative cell surface coreceptor for growth factors, extracellular matrix proteins, proteases and anti-proteases. Mutations in this gene are associated with omodysplasia 1. [provided by RefSeq, Nov 2016]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit neonatal lethality, decreased fetal weight, short long bones, small skull, small snout, cleft palate and decreased chondrocyte proliferation. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ablim1	G	T	19: 57,025,691 (GRCm39)	R851S	probably damaging	Het
Acap2	C	A	16: 30,929,763 (GRCm39)	A407S	probably damaging	Het
Adam26a	A	T	8: 44,021,635 (GRCm39)	S618R	probably benign	Het
Adamtsl5	T	C	10: 80,180,896 (GRCm39)	Y89C	probably damaging	Het
Aebp2	T	A	6: 140,588,021 (GRCm39)	S364T	probably damaging	Het
Ankfy1	A	G	11: 72,621,401 (GRCm39)	E229G	probably benign	Het
Arhgap27	G	T	11: 103,251,511 (GRCm39)	D72E	probably benign	Het
Arhgap33	T	C	7: 30,230,950 (GRCm39)	E191G	probably null	Het
Atp6v0a1	C	T	11: 100,946,427 (GRCm39)	H807Y	possibly damaging	Het
Ccdc113	A	C	8: 96,272,605 (GRCm39)	E237D	probably benign	Het
Cd200r2	T	A	16: 44,729,420 (GRCm39)	I25K	probably benign	Het
Cd300c2	A	G	11: 114,887,775 (GRCm39)	V209A	probably damaging	Het
Cdkn2d	T	A	9: 21,200,383 (GRCm39)	E129D	probably benign	Het
Cfap251	A	G	5: 123,460,533 (GRCm39)	Y1165C	probably damaging	Het
Chd9	A	T	8: 91,712,741 (GRCm39)	N855Y	unknown	Het
Cntn3	A	G	6: 102,254,196 (GRCm39)	C249R	probably damaging	Het
Col12a1	T	C	9: 79,527,266 (GRCm39)	E2688G	possibly damaging	Het
Copb2	C	T	9: 98,464,901 (GRCm39)	T612I	probably benign	Het
Cplx1	A	T	5: 108,673,378 (GRCm39)	D29E	possibly damaging	Het
Cracd	A	G	5: 77,006,555 (GRCm39)	K972R	unknown	Het
Cstf3	A	T	2: 104,494,684 (GRCm39)	R645*	probably null	Het
Ctdp1	A	T	18: 80,492,550 (GRCm39)	Y648*	probably null	Het
Daam1	T	A	12: 71,990,855 (GRCm39)	D156E	unknown	Het
Dbn1	G	A	13: 55,622,824 (GRCm39)	P599L	probably damaging	Het
Diaph1	C	A	18: 37,987,589 (GRCm39)	V1056F	probably damaging	Het
Dzip3	A	T	16: 48,748,707 (GRCm39)	D870E	probably damaging	Het
Efcab12	T	C	6: 115,800,331 (GRCm39)	T231A	possibly damaging	Het
Efl1	A	C	7: 82,412,596 (GRCm39)	D995A	probably benign	Het
Fam186a	T	C	15: 99,842,393 (GRCm39)	T1284A	possibly damaging	Het
Fbxo33	T	C	12: 59,251,708 (GRCm39)	E269G	probably benign	Het
Foxj3	T	A	4: 119,483,540 (GRCm39)	M604K	unknown	Het
Gabra4	A	G	5: 71,814,463 (GRCm39)	S86P	unknown	Het
Gnas	G	A	2: 174,140,639 (GRCm39)	W269*	probably null	Het
Gprin3	T	C	6: 59,331,236 (GRCm39)	K357R	possibly damaging	Het
Grip1	G	T	10: 119,811,906 (GRCm39)	A286S	possibly damaging	Het
Grm4	A	T	17: 27,721,688 (GRCm39)	V151E	probably damaging	Het
Gucy1b1	A	T	3: 81,942,065 (GRCm39)	S565T	possibly damaging	Het
Hace1	T	C	10: 45,525,014 (GRCm39)	V260A	probably benign	Het
Hepacam2	A	G	6: 3,486,940 (GRCm39)	I139T	probably damaging	Het
Hspa4l	T	C	3: 40,727,057 (GRCm39)	I486T	probably benign	Het
Igkv8-19	T	C	6: 70,317,866 (GRCm39)	Y120C	probably damaging	Het
Iglv2	C	T	16: 19,079,548 (GRCm39)		probably benign	Het
Igsf10	A	T	3: 59,237,106 (GRCm39)	L1025H	probably damaging	Het
Itpkb	A	G	1: 180,161,752 (GRCm39)	N626S	probably benign	Het
Jarid2	C	T	13: 45,068,253 (GRCm39)	R1092W	possibly damaging	Het
Klc3	C	T	7: 19,132,023 (GRCm39)	W118*	probably null	Het
Klhl25	C	T	7: 75,516,741 (GRCm39)	T549I	probably damaging	Het
Krtap6-2	T	A	16: 89,216,763 (GRCm39)	Y68F	unknown	Het
Mtcl1	T	C	17: 66,673,347 (GRCm39)	N1121D	probably benign	Het
Ncbp3	A	G	11: 72,961,668 (GRCm39)	K314R	probably benign	Het
Nop2	T	C	6: 125,121,272 (GRCm39)	W685R	probably benign	Het
Orc1	T	A	4: 108,447,874 (GRCm39)	D40E	probably benign	Het
Pappa2	G	T	1: 158,684,948 (GRCm39)	N730K	probably damaging	Het
Parpbp	A	G	10: 87,960,815 (GRCm39)	S224P	possibly damaging	Het
Pdgfc	A	G	3: 80,944,792 (GRCm39)	R17G	probably benign	Het
Pfpl	G	C	19: 12,406,297 (GRCm39)	E183Q	probably damaging	Het
Pik3r6	T	A	11: 68,424,358 (GRCm39)	L321*	probably null	Het
Pnp2	T	C	14: 51,197,006 (GRCm39)	W31R	probably damaging	Het
Prr12	T	C	7: 44,696,954 (GRCm39)	Y987C	unknown	Het
Prr27	C	A	5: 87,990,994 (GRCm39)	P202Q	probably benign	Het
Prss23	T	C	7: 89,159,683 (GRCm39)	I129V	probably damaging	Het
Rhno1	T	C	6: 128,336,119 (GRCm39)	T39A	probably damaging	Het
Rps2	A	T	17: 24,940,810 (GRCm39)	R279*	probably null	Het
Ski	T	C	4: 155,244,344 (GRCm39)	K427R	probably damaging	Het
Slc23a3	ATT	ATTT	1: 75,109,925 (GRCm39)		probably null	Het
Slc26a7	C	T	4: 14,546,372 (GRCm39)	G319D	probably damaging	Het
Slc7a6os	A	G	8: 106,937,523 (GRCm39)	V8A	probably damaging	Het
Smim8	A	C	4: 34,771,265 (GRCm39)	I43S	probably damaging	Het
Sox5	T	C	6: 143,819,842 (GRCm39)	K400R	probably damaging	Het
Tab1	G	A	15: 80,032,943 (GRCm39)	V76M	probably damaging	Het
Taf2	A	C	15: 54,894,440 (GRCm39)		probably null	Het
Taf5	G	A	19: 47,059,434 (GRCm39)	V193M	probably damaging	Het
Tm2d1	A	T	4: 98,246,261 (GRCm39)	S180R	probably damaging	Het
Ttc12	A	G	9: 49,368,166 (GRCm39)	F287S	probably damaging	Het
Ubqln4	G	A	3: 88,473,185 (GRCm39)		probably null	Het
Ubr3	T	C	2: 69,839,497 (GRCm39)	V1537A	probably benign	Het
Ugt8a	A	G	3: 125,708,900 (GRCm39)	L70P	probably damaging	Het
Vps26a	A	T	10: 62,316,433 (GRCm39)	N51K	probably benign	Het
Xkr5	T	A	8: 18,990,749 (GRCm39)	T173S	probably benign	Het
Zfp354c	A	G	11: 50,706,239 (GRCm39)	C279R	probably damaging	Het
Zfp65	T	A	13: 67,856,478 (GRCm39)	H267L	probably damaging	Het

Other mutations in Gpc6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00597:Gpc6	APN	14	118,188,646 (GRCm39)	missense	probably benign	0.01
IGL00671:Gpc6	APN	14	117,424,199 (GRCm39)	missense	probably benign	0.01
IGL00928:Gpc6	APN	14	117,163,370 (GRCm39)	missense	possibly damaging	0.86
IGL01343:Gpc6	APN	14	117,424,224 (GRCm39)	missense	possibly damaging	0.54
IGL01545:Gpc6	APN	14	118,202,242 (GRCm39)	missense	probably damaging	1.00
IGL02797:Gpc6	APN	14	117,163,394 (GRCm39)	missense	probably damaging	0.98
PIT1430001:Gpc6	UTSW	14	118,188,594 (GRCm39)	nonsense	probably null
R0577:Gpc6	UTSW	14	117,673,420 (GRCm39)	missense	probably benign	0.03
R0611:Gpc6	UTSW	14	118,212,430 (GRCm39)	missense	probably null
R0636:Gpc6	UTSW	14	117,861,905 (GRCm39)	missense	probably benign	0.37
R2152:Gpc6	UTSW	14	117,163,504 (GRCm39)	missense	probably benign	0.00
R2242:Gpc6	UTSW	14	117,424,199 (GRCm39)	missense	probably benign	0.01
R2266:Gpc6	UTSW	14	118,125,932 (GRCm39)	critical splice acceptor site	probably null
R2267:Gpc6	UTSW	14	118,125,932 (GRCm39)	critical splice acceptor site	probably null
R2269:Gpc6	UTSW	14	118,125,932 (GRCm39)	critical splice acceptor site	probably null
R3788:Gpc6	UTSW	14	117,861,878 (GRCm39)	missense	probably damaging	0.98
R4255:Gpc6	UTSW	14	118,188,553 (GRCm39)	missense	probably benign	0.15
R4276:Gpc6	UTSW	14	117,673,328 (GRCm39)	missense	probably damaging	0.99
R4411:Gpc6	UTSW	14	118,188,590 (GRCm39)	missense	probably benign	0.45
R4626:Gpc6	UTSW	14	118,202,255 (GRCm39)	nonsense	probably null
R4993:Gpc6	UTSW	14	117,861,951 (GRCm39)	missense	possibly damaging	0.93
R5070:Gpc6	UTSW	14	117,424,181 (GRCm39)	missense	probably benign	0.01
R6007:Gpc6	UTSW	14	118,188,673 (GRCm39)	missense	probably damaging	1.00
R6058:Gpc6	UTSW	14	118,202,182 (GRCm39)	missense	probably damaging	1.00
R6488:Gpc6	UTSW	14	118,202,125 (GRCm39)	missense	possibly damaging	0.73
R6901:Gpc6	UTSW	14	118,188,629 (GRCm39)	missense	possibly damaging	0.87
R6981:Gpc6	UTSW	14	117,861,960 (GRCm39)	missense	probably damaging	0.98
R7200:Gpc6	UTSW	14	118,202,268 (GRCm39)	missense	probably benign	0.08
R8348:Gpc6	UTSW	14	117,673,232 (GRCm39)	missense	probably damaging	1.00
R8354:Gpc6	UTSW	14	117,163,391 (GRCm39)	missense	probably damaging	0.98
R8413:Gpc6	UTSW	14	118,129,761 (GRCm39)	missense	possibly damaging	0.93
R8454:Gpc6	UTSW	14	117,163,391 (GRCm39)	missense	probably damaging	0.98
R8518:Gpc6	UTSW	14	117,163,384 (GRCm39)	missense	probably benign	0.10
R9009:Gpc6	UTSW	14	117,424,217 (GRCm39)	missense	possibly damaging	0.84
R9112:Gpc6	UTSW	14	117,424,088 (GRCm39)	missense	probably benign	0.01
R9481:Gpc6	UTSW	14	117,163,432 (GRCm39)	missense	probably benign
R9790:Gpc6	UTSW	14	117,163,435 (GRCm39)	missense	probably damaging	0.98
R9791:Gpc6	UTSW	14	117,163,435 (GRCm39)	missense	probably damaging	0.98

Predicted Primers

PCR Primer
(F):5'- CATCTGAGATAGCAGGGCTG -3'
(R):5'- GCATGTACATTGTGCCTCAG -3'

Sequencing Primer
(F):5'- TGGTTCTGAGGTCACCACAAC -3'
(R):5'- ATGTACATTGTGCCTCAGACCGG -3'

Posted On

2022-11-14