Mutagenetix > Incidental Mutation

Incidental Mutation 'R6223:Col10a1'

504152

Institutional Source

Beutler Lab

Gene Symbol

Col10a1

Ensembl Gene

ENSMUSG00000039462

Gene Name

collagen, type X, alpha 1

Synonyms

Col10, Col10a-1

MMRRC Submission

044354-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.121) question?

Stock #

R6223 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

34265977-34273081 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 34271183 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 385 (D385V)

Ref Sequence

ENSEMBL: ENSMUSP00000101150 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000047885] [ENSMUST00000099973] [ENSMUST00000105511] [ENSMUST00000105512] [ENSMUST00000213269]

AlphaFold

Q05306

Predicted Effect

probably benign
Transcript: ENSMUST00000047885

SMART Domains

Protein: ENSMUSP00000047126
Gene: ENSMUSG00000039480

Domain	Start	End	E-Value	Type
Pfam:5_nucleotid	1	382	2.6e-58	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000099973

SMART Domains

Protein: ENSMUSP00000097553
Gene: ENSMUSG00000039480

Domain	Start	End	E-Value	Type
Pfam:5_nucleotid	1	189	8.8e-25	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000105511
AA Change: D385V

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

SMART Domains

Protein: ENSMUSP00000101150
Gene: ENSMUSG00000039462
AA Change: D385V

Domain	Start	End	E-Value	Type
signal peptide	1	18	N/A	INTRINSIC
low complexity region	60	101	N/A	INTRINSIC
Pfam:Collagen	103	155	1.4e-9	PFAM
Pfam:Collagen	153	218	1.4e-8	PFAM
Pfam:Collagen	193	250	2.6e-9	PFAM
Pfam:Collagen	206	264	3.8e-8	PFAM
low complexity region	282	323	N/A	INTRINSIC
internal_repeat_2	329	361	2.25e-6	PROSPERO
internal_repeat_1	331	365	5.9e-14	PROSPERO
low complexity region	368	383	N/A	INTRINSIC
low complexity region	391	410	N/A	INTRINSIC
Pfam:Collagen	413	483	9.3e-10	PFAM
low complexity region	487	517	N/A	INTRINSIC
C1Q	545	680	2.85e-79	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000105512

SMART Domains

Protein: ENSMUSP00000101151
Gene: ENSMUSG00000039480

Domain	Start	End	E-Value	Type
Pfam:5_nucleotid	1	372	8.7e-54	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130290

Predicted Effect

probably benign
Transcript: ENSMUST00000213269

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.4%
20x: 95.6%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the alpha chain of type X collagen, a short chain collagen expressed by hypertrophic chondrocytes during endochondral ossification. Unlike type VIII collagen, the other short chain collagen, type X collagen is a homotrimer. Mutations in this gene are associated with Schmid type metaphyseal chondrodysplasia (SMCD) and Japanese type spondylometaphyseal dysplasia (SMD). [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted null mutations may exhibit abnormal trabecular bone, thinner growth plate resting zone and articular cartilage, and altered bone content. Mice homozygous for another knock-out allele exhibit altered B and T cell populations and TH1/TH2responses. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
6820408C15Rik	A	C	2: 152,269,873 (GRCm39)	R8S	probably benign	Het
Abca8b	A	G	11: 109,868,672 (GRCm39)	V164A	probably benign	Het
Acadm	C	A	3: 153,644,186 (GRCm39)		probably null	Het
Ap3b2	G	A	7: 81,123,210 (GRCm39)	R435*	probably null	Het
Art2b	A	G	7: 101,229,158 (GRCm39)	F247S	possibly damaging	Het
C1rb	T	A	6: 124,551,539 (GRCm39)	D216E	probably benign	Het
Casz1	C	A	4: 149,017,840 (GRCm39)	D90E	probably damaging	Het
Ccdc13	A	G	9: 121,627,975 (GRCm39)		probably benign	Het
Cdc25a	C	A	9: 109,718,842 (GRCm39)	P409T	possibly damaging	Het
Cidea	A	C	18: 67,491,809 (GRCm39)	K23T	possibly damaging	Het
Clspn	T	A	4: 126,479,961 (GRCm39)	D1101E	probably damaging	Het
Crat	C	T	2: 30,297,042 (GRCm39)	V304I	probably benign	Het
Cyp2d26	A	T	15: 82,675,918 (GRCm39)	W265R	probably benign	Het
Dock8	A	T	19: 25,138,416 (GRCm39)	Y1247F	probably benign	Het
Dync2i1	T	C	12: 116,221,078 (GRCm39)	D11G	possibly damaging	Het
Eed	A	G	7: 89,605,495 (GRCm39)	Y365H	probably damaging	Het
Fabp5	T	A	3: 10,080,170 (GRCm39)	F73L	probably benign	Het
Fbn1	C	T	2: 125,254,591 (GRCm39)	C224Y	possibly damaging	Het
Ggcx	T	C	6: 72,406,588 (GRCm39)	F684L	probably damaging	Het
Glrp1	G	A	1: 88,431,164 (GRCm39)	Q69*	probably null	Het
Gm29797	T	C	2: 181,300,850 (GRCm39)	V115A	possibly damaging	Het
Gtf3c1	C	T	7: 125,275,797 (GRCm39)	R543K	probably benign	Het
Ifih1	T	C	2: 62,428,603 (GRCm39)	I891V	probably benign	Het
Ifnar2	C	T	16: 91,184,876 (GRCm39)	T89M	probably damaging	Het
Kat6a	C	A	8: 23,430,442 (GRCm39)	N1932K	unknown	Het
Mgat5	A	T	1: 127,310,716 (GRCm39)	D210V	possibly damaging	Het
Mmel1	A	G	4: 154,956,159 (GRCm39)		probably null	Het
Myh3	G	T	11: 66,988,843 (GRCm39)	V1499L	probably benign	Het
Ncan	A	C	8: 70,562,604 (GRCm39)	D551E	probably benign	Het
Nol11	G	T	11: 107,062,442 (GRCm39)	T598K	possibly damaging	Het
Olfml3	G	A	3: 103,643,776 (GRCm39)	R202W	probably damaging	Het
Or2w4	G	A	13: 21,795,536 (GRCm39)	T201I	probably benign	Het
Or4e2	A	G	14: 52,688,136 (GRCm39)	R89G	probably benign	Het
Pcdh9	T	C	14: 93,253,169 (GRCm39)	K1131E	probably benign	Het
Pcolce	A	G	5: 137,603,561 (GRCm39)	M424T	probably damaging	Het
Pi16	C	A	17: 29,546,413 (GRCm39)	S397*	probably null	Het
Pi4ka	A	T	16: 17,175,435 (GRCm39)	Y464*	probably null	Het
Pik3c2b	T	A	1: 132,998,095 (GRCm39)	L324M	probably damaging	Het
Prdm2	T	C	4: 142,868,777 (GRCm39)	N179S	probably benign	Het
Prss56	C	T	1: 87,113,134 (GRCm39)	P183S	probably benign	Het
Prx	T	G	7: 27,216,261 (GRCm39)	M393R	probably damaging	Het
Qpctl	T	C	7: 18,877,134 (GRCm39)	D328G	probably damaging	Het
Qser1	A	G	2: 104,617,993 (GRCm39)	S940P	probably benign	Het
Rchy1	G	A	5: 92,105,826 (GRCm39)	R41W	probably damaging	Het
Scp2d1	T	C	2: 144,665,868 (GRCm39)	I69T	possibly damaging	Het
Sirpb1a	A	G	3: 15,444,086 (GRCm39)	V388A	probably benign	Het
Ssu2	G	T	6: 112,353,409 (GRCm39)	C238*	probably null	Het
Stub1	C	T	17: 26,051,787 (GRCm39)	G14D	probably damaging	Het
Tab1	T	A	15: 80,032,464 (GRCm39)	C24S	probably damaging	Het
Tdrd1	T	C	19: 56,854,282 (GRCm39)	V1076A	probably damaging	Het
Tex10	T	C	4: 48,468,525 (GRCm39)	R134G	probably damaging	Het
Tg	T	A	15: 66,579,771 (GRCm39)	N1525K	probably benign	Het
Tll2	G	A	19: 41,124,391 (GRCm39)	T208I	possibly damaging	Het
Tmem232	T	C	17: 65,807,191 (GRCm39)	M1V	probably null	Het
Ttc7b	A	G	12: 100,353,368 (GRCm39)		probably null	Het
Ubb	A	G	11: 62,443,351 (GRCm39)	E127G	possibly damaging	Het
Ulk2	A	T	11: 61,678,330 (GRCm39)	Y796*	probably null	Het
Vdac2	G	A	14: 21,895,246 (GRCm39)	G265R	possibly damaging	Het
Vmn2r45	A	T	7: 8,486,301 (GRCm39)	V329E	probably benign	Het
Zbtb47	G	A	9: 121,592,853 (GRCm39)	R391Q	possibly damaging	Het

Other mutations in Col10a1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL03005:Col10a1	APN	10	34,271,734 (GRCm39)	missense	probably damaging	1.00
IGL03028:Col10a1	APN	10	34,271,012 (GRCm39)	missense	probably benign	0.19
R0580:Col10a1	UTSW	10	34,270,948 (GRCm39)	missense	probably benign	0.31
R0691:Col10a1	UTSW	10	34,271,692 (GRCm39)	missense	possibly damaging	0.94
R1187:Col10a1	UTSW	10	34,270,834 (GRCm39)	missense	probably benign	0.13
R1597:Col10a1	UTSW	10	34,271,074 (GRCm39)	missense	probably damaging	0.99
R1724:Col10a1	UTSW	10	34,271,714 (GRCm39)	missense	probably damaging	1.00
R1826:Col10a1	UTSW	10	34,270,645 (GRCm39)	missense	probably damaging	1.00
R1834:Col10a1	UTSW	10	34,271,011 (GRCm39)	missense	probably damaging	1.00
R2156:Col10a1	UTSW	10	34,271,696 (GRCm39)	missense	probably benign	0.30
R3687:Col10a1	UTSW	10	34,271,494 (GRCm39)	missense	probably benign	0.12
R4208:Col10a1	UTSW	10	34,271,539 (GRCm39)	missense	probably damaging	0.99
R4929:Col10a1	UTSW	10	34,271,120 (GRCm39)	missense	probably benign	0.00
R5411:Col10a1	UTSW	10	34,270,553 (GRCm39)	missense	probably damaging	1.00
R5433:Col10a1	UTSW	10	34,266,735 (GRCm39)	intron	probably benign
R5481:Col10a1	UTSW	10	34,271,660 (GRCm39)	missense	probably benign	0.09
R6036:Col10a1	UTSW	10	34,271,278 (GRCm39)	missense	probably benign
R6036:Col10a1	UTSW	10	34,271,278 (GRCm39)	missense	probably benign
R6208:Col10a1	UTSW	10	34,270,582 (GRCm39)	missense	possibly damaging	0.69
R7019:Col10a1	UTSW	10	34,270,947 (GRCm39)	missense	probably damaging	0.96
R7642:Col10a1	UTSW	10	34,271,638 (GRCm39)	missense	probably benign	0.00
R7784:Col10a1	UTSW	10	34,270,214 (GRCm39)	missense	unknown
R8072:Col10a1	UTSW	10	34,266,663 (GRCm39)	missense	unknown
R8711:Col10a1	UTSW	10	34,270,824 (GRCm39)	missense	probably damaging	1.00
Z1176:Col10a1	UTSW	10	34,271,174 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TTTGGAAAACAAGGCTTGCC -3'
(R):5'- TTGGACCTGCCTCACCATTG -3'

Sequencing Primer
(F):5'- AACAAGGCTTGCCAGGTTTG -3'
(R):5'- ACCATTGTGTCCAGGCAC -3'

Posted On

2018-02-28