Mutagenetix > Incidental Mutation

Incidental Mutation 'R1826:Col10a1'

206807

Institutional Source

Beutler Lab

Gene Symbol

Col10a1

Ensembl Gene

ENSMUSG00000039462

Gene Name

collagen, type X, alpha 1

Synonyms

Col10a-1, Col10

MMRRC Submission

039853-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.125) question?

Stock #

R1826 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

34389981-34397085 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 34394649 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Cysteine at position 206 (G206C)

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: G206C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000101150
Gene: ENSMUSG00000039462
AA Change: G206C

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

Meta Mutation Damage Score

0.9550

Coding Region Coverage

1x: 97.5%
3x: 96.8%
10x: 95.1%
20x: 92.0%

Validation Efficiency

95% (116/122)

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: 112 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc2	T	C	19: 43,822,014 (GRCm38)	S917P	probably benign	Het
Acsbg1	C	T	9: 54,622,556 (GRCm38)	V256M	possibly damaging	Het
Adam34	T	A	8: 43,651,342 (GRCm38)	D422V	probably damaging	Het
Adam6a	T	A	12: 113,546,122 (GRCm38)	V705E	possibly damaging	Het
Adamts12	C	A	15: 11,071,520 (GRCm38)	P50Q	probably benign	Het
Arfgap3	C	T	15: 83,303,102 (GRCm38)		probably null	Het
Aspg	T	A	12: 112,123,418 (GRCm38)	D463E	probably damaging	Het
Atad2b	G	A	12: 4,974,094 (GRCm38)	S73N	probably benign	Het
Atp11a	T	C	8: 12,846,154 (GRCm38)	L788P	probably damaging	Het
B3gnt8	T	C	7: 25,628,763 (GRCm38)	F206S	probably damaging	Het
Baz2b	T	C	2: 59,968,733 (GRCm38)	E349G	probably benign	Het
Bmp2k	A	T	5: 97,061,402 (GRCm38)		probably benign	Het
Camta2	A	G	11: 70,683,308 (GRCm38)	F128L	probably damaging	Het
Ccdc88a	A	T	11: 29,489,637 (GRCm38)	Q30L	possibly damaging	Het
Cdh1	T	C	8: 106,666,266 (GRCm38)	M794T	probably benign	Het
Cdh5	A	G	8: 104,131,091 (GRCm38)	N383S	possibly damaging	Het
Cep85l	T	C	10: 53,348,812 (GRCm38)	D227G	possibly damaging	Het
Clec4e	A	G	6: 123,283,632 (GRCm38)	S156P	probably damaging	Het
Col4a2	T	C	8: 11,313,509 (GRCm38)		probably null	Het
Copg2	A	G	6: 30,812,842 (GRCm38)	M517T	probably benign	Het
Cyp2f2	T	A	7: 27,132,562 (GRCm38)	L414Q	probably damaging	Het
Dact1	G	A	12: 71,318,344 (GRCm38)	G596D	probably damaging	Het
Dcaf13	T	C	15: 39,118,899 (GRCm38)	C87R	probably damaging	Het
Dchs1	T	G	7: 105,757,627 (GRCm38)	T2224P	probably damaging	Het
Dnah12	A	G	14: 26,711,019 (GRCm38)	M429V	probably benign	Het
Dppa2	G	A	16: 48,317,348 (GRCm38)	R231H	probably damaging	Het
Elavl4	T	C	4: 110,251,292 (GRCm38)	D78G	probably damaging	Het
Enthd1	T	C	15: 80,474,281 (GRCm38)	E346G	probably damaging	Het
Exoc3l	A	T	8: 105,293,618 (GRCm38)	I225N	probably damaging	Het
Fasn	C	T	11: 120,808,499 (GRCm38)		probably benign	Het
Fbxl7	G	A	15: 26,552,765 (GRCm38)	R139C	possibly damaging	Het
Fbxw15	C	A	9: 109,559,714 (GRCm38)		probably null	Het
Flnc	A	G	6: 29,455,185 (GRCm38)	T1971A	probably damaging	Het
Fnip1	T	G	11: 54,466,164 (GRCm38)	V33G	probably damaging	Het
Foxn2	A	G	17: 88,486,805 (GRCm38)	E390G	possibly damaging	Het
Fry	C	T	5: 150,436,709 (GRCm38)	S1940L	possibly damaging	Het
Fzd3	A	T	14: 65,253,106 (GRCm38)	D9E	probably benign	Het
Gabrd	T	C	4: 155,386,486 (GRCm38)	Y255C	probably damaging	Het
Garem1	A	T	18: 21,129,452 (GRCm38)	F768L	probably benign	Het
Gas2	T	A	7: 51,943,673 (GRCm38)	L167Q	probably damaging	Het
Gm16391	A	G	17: 76,284,423 (GRCm38)		noncoding transcript	Het
Gm1979	A	T	5: 26,001,242 (GRCm38)	N113K	probably damaging	Het
Gpr83	G	T	9: 14,868,333 (GRCm38)	C269F	possibly damaging	Het
Hdac4	T	A	1: 91,984,699 (GRCm38)	N352Y	probably damaging	Het
Hdac9	A	G	12: 34,429,492 (GRCm38)		probably benign	Het
Hhipl2	G	A	1: 183,436,344 (GRCm38)	S673N	probably benign	Het
Iffo2	T	A	4: 139,614,065 (GRCm38)	S417T	probably benign	Het
Itgb5	G	T	16: 33,865,560 (GRCm38)	R90L	possibly damaging	Het
Jade1	T	G	3: 41,613,213 (GRCm38)	L572W	probably damaging	Het
Kcnh1	T	A	1: 192,413,068 (GRCm38)	M478K	possibly damaging	Het
Kcnma1	C	A	14: 23,330,929 (GRCm38)	D903Y	probably damaging	Het
Kcnq4	T	A	4: 120,704,504 (GRCm38)	H456L	probably benign	Het
Kif9	C	A	9: 110,517,633 (GRCm38)	T613K	probably benign	Het
Krt36	T	G	11: 100,103,030 (GRCm38)		probably benign	Het
Kyat3	A	T	3: 142,723,179 (GRCm38)	D89V	possibly damaging	Het
Lnpep	A	T	17: 17,562,836 (GRCm38)	F568I	probably damaging	Het
Lpl	T	C	8: 68,902,291 (GRCm38)	F444L	possibly damaging	Het
Lrp1	A	T	10: 127,553,707 (GRCm38)	V3153E	probably damaging	Het
Lrrn1	A	T	6: 107,567,568 (GRCm38)	N109I	probably benign	Het
Ltn1	A	G	16: 87,415,616 (GRCm38)	Y686H	probably damaging	Het
Mcoln2	A	C	3: 146,175,472 (GRCm38)	D166A	possibly damaging	Het
Ms4a6b	A	T	19: 11,523,934 (GRCm38)	I103F	probably damaging	Het
Mtmr10	T	G	7: 64,337,466 (GRCm38)	S585A	probably benign	Het
Mx1	T	C	16: 97,455,637 (GRCm38)	N114S	possibly damaging	Het
Mysm1	A	T	4: 94,970,686 (GRCm38)	N75K	probably benign	Het
Nkx1-1	A	G	5: 33,433,933 (GRCm38)	V15A	unknown	Het
Nlrp1a	T	A	11: 71,107,980 (GRCm38)		probably benign	Het
Nlrp1a	G	A	11: 71,122,747 (GRCm38)	T559I	possibly damaging	Het
Oas1f	A	G	5: 120,855,589 (GRCm38)	K288R	probably benign	Het
Or10q1	T	A	19: 13,749,347 (GRCm38)	D80E	probably benign	Het
Or55b3	A	G	7: 102,477,513 (GRCm38)	L119P	probably damaging	Het
Or9e1	T	A	11: 58,841,431 (GRCm38)	C106S	probably benign	Het
Pcdhb2	T	A	18: 37,295,985 (GRCm38)	V337D	probably damaging	Het
Pcdhb5	C	T	18: 37,321,469 (GRCm38)	R301*	probably null	Het
Phf12	T	C	11: 78,024,954 (GRCm38)		probably benign	Het
Pik3c2a	C	T	7: 116,368,117 (GRCm38)	D862N	probably benign	Het
Pkhd1l1	T	A	15: 44,503,345 (GRCm38)	L740I	possibly damaging	Het
Ppp1r9a	A	T	6: 5,111,060 (GRCm38)		probably benign	Het
Prg4	T	C	1: 150,452,009 (GRCm38)	D820G	probably benign	Het
Prmt9	C	T	8: 77,555,674 (GRCm38)	Q67*	probably null	Het
Prob1	T	C	18: 35,653,575 (GRCm38)	E542G	possibly damaging	Het
Pttg1	A	G	11: 43,420,366 (GRCm38)	V188A	probably damaging	Het
Rassf1	T	A	9: 107,558,193 (GRCm38)	L260H	probably damaging	Het
Rbm5	T	A	9: 107,742,414 (GRCm38)	Q766L	probably damaging	Het
Rbms3	T	A	9: 116,822,868 (GRCm38)	Y137F	probably damaging	Het
Rccd1	T	C	7: 80,320,218 (GRCm38)		probably benign	Het
Rnf182	G	A	13: 43,668,534 (GRCm38)	W187*	probably null	Het
S100a11	A	T	3: 93,526,121 (GRCm38)	I91F	probably benign	Het
Setd4	T	A	16: 93,591,299 (GRCm38)	K100*	probably null	Het
Simc1	T	A	13: 54,524,639 (GRCm38)	C267S	probably benign	Het
Slc16a1	G	T	3: 104,650,939 (GRCm38)	A91S	probably benign	Het
Slc36a1	A	G	11: 55,220,453 (GRCm38)	N133S	probably benign	Het
Ssxb16	T	A	X: 8,880,705 (GRCm38)	Y133*	probably null	Het
Svil	C	T	18: 5,063,383 (GRCm38)	P885S	probably benign	Het
Svop	A	T	5: 114,060,056 (GRCm38)		probably null	Het
Taar7d	T	C	10: 24,027,576 (GRCm38)	Y119H	probably damaging	Het
Tasor2	T	A	13: 3,581,759 (GRCm38)	N914I	probably damaging	Het
Tgfb3	T	C	12: 86,062,044 (GRCm38)	T304A	probably benign	Het
Tmem94	C	A	11: 115,793,213 (GRCm38)	C786*	probably null	Het
Tnfrsf4	T	A	4: 156,016,279 (GRCm38)		probably null	Het
Tns1	C	A	1: 73,953,634 (GRCm38)	M1I	probably null	Het
Trappc13	C	T	13: 104,169,819 (GRCm38)		probably null	Het
Trim72	T	C	7: 128,007,844 (GRCm38)	F182L	possibly damaging	Het
Ttc6	T	C	12: 57,660,247 (GRCm38)	S647P	probably benign	Het
Tulp1	A	G	17: 28,356,367 (GRCm38)	L400P	possibly damaging	Het
Vegfc	C	T	8: 54,181,312 (GRCm38)	T342M	possibly damaging	Het
Vit	T	A	17: 78,534,676 (GRCm38)	V15E	probably benign	Het
Vps13d	A	T	4: 145,155,003 (GRCm38)	M1334K	probably damaging	Het
Zfp280d	T	C	9: 72,298,780 (GRCm38)	V23A	probably damaging	Het
Zfp608	A	G	18: 54,898,576 (GRCm38)	I764T	probably benign	Het
Zfp94	T	C	7: 24,309,115 (GRCm38)	Y33C	probably damaging	Het
Zfyve26	T	A	12: 79,269,049 (GRCm38)	I1218F	probably damaging	Het

Other mutations in Col10a1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL03005:Col10a1	APN	10	34,395,738 (GRCm38)	missense	probably damaging	1.00
IGL03028:Col10a1	APN	10	34,395,016 (GRCm38)	missense	probably benign	0.19
R0580:Col10a1	UTSW	10	34,394,952 (GRCm38)	missense	probably benign	0.31
R0691:Col10a1	UTSW	10	34,395,696 (GRCm38)	missense	possibly damaging	0.94
R1187:Col10a1	UTSW	10	34,394,838 (GRCm38)	missense	probably benign	0.13
R1597:Col10a1	UTSW	10	34,395,078 (GRCm38)	missense	probably damaging	0.99
R1724:Col10a1	UTSW	10	34,395,718 (GRCm38)	missense	probably damaging	1.00
R1834:Col10a1	UTSW	10	34,395,015 (GRCm38)	missense	probably damaging	1.00
R2156:Col10a1	UTSW	10	34,395,700 (GRCm38)	missense	probably benign	0.30
R3687:Col10a1	UTSW	10	34,395,498 (GRCm38)	missense	probably benign	0.12
R4208:Col10a1	UTSW	10	34,395,543 (GRCm38)	missense	probably damaging	0.99
R4929:Col10a1	UTSW	10	34,395,124 (GRCm38)	missense	probably benign	0.00
R5411:Col10a1	UTSW	10	34,394,557 (GRCm38)	missense	probably damaging	1.00
R5433:Col10a1	UTSW	10	34,390,739 (GRCm38)	intron	probably benign
R5481:Col10a1	UTSW	10	34,395,664 (GRCm38)	missense	probably benign	0.09
R6036:Col10a1	UTSW	10	34,395,282 (GRCm38)	missense	probably benign
R6036:Col10a1	UTSW	10	34,395,282 (GRCm38)	missense	probably benign
R6208:Col10a1	UTSW	10	34,394,586 (GRCm38)	missense	possibly damaging	0.69
R6223:Col10a1	UTSW	10	34,395,187 (GRCm38)	missense	probably damaging	1.00
R7019:Col10a1	UTSW	10	34,394,951 (GRCm38)	missense	probably damaging	0.96
R7642:Col10a1	UTSW	10	34,395,642 (GRCm38)	missense	probably benign	0.00
R7784:Col10a1	UTSW	10	34,394,218 (GRCm38)	missense	unknown
R8072:Col10a1	UTSW	10	34,390,667 (GRCm38)	missense	unknown
R8711:Col10a1	UTSW	10	34,394,828 (GRCm38)	missense	probably damaging	1.00
Z1176:Col10a1	UTSW	10	34,395,178 (GRCm38)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CCCAGCTGGAATTTCTGTGC -3'
(R):5'- TGGAGGACCAGCTATTCCTG -3'

Sequencing Primer
(F):5'- TTCTGTGCCAGGAAAACCTG -3'
(R):5'- CTGACCAGGGGATCCAATG -3'

Posted On

2014-06-23