Mutagenetix > Incidental Mutation

Incidental Mutation 'R7642:Col10a1'

590300

Institutional Source

Beutler Lab

Gene Symbol

Col10a1

Ensembl Gene

ENSMUSG00000039462

Gene Name

collagen, type X, alpha 1

Synonyms

Col10, Col10a-1

MMRRC Submission

045645-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.108) question?

Stock #

R7642 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

34265977-34273081 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 34271638 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Valine at position 537 (M537V)

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 benign
Transcript: ENSMUST00000105511
AA Change: M537V

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

SMART Domains

Protein: ENSMUSP00000101150
Gene: ENSMUSG00000039462
AA Change: M537V

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

probably benign
Transcript: ENSMUST00000213269

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.2%

Validation Efficiency

100% (48/48)

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: 51 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ap3b1	T	C	13: 94,613,540 (GRCm39)	S680P	probably benign	Het
Carmil1	T	C	13: 24,251,189 (GRCm39)	T844A	probably benign	Het
Cfap57	C	T	4: 118,472,128 (GRCm39)	V84I	probably benign	Het
Clca4a	A	T	3: 144,659,512 (GRCm39)	D781E	probably benign	Het
Col5a2	A	G	1: 45,415,248 (GRCm39)	M1497T	probably benign	Het
Csmd1	T	A	8: 16,135,192 (GRCm39)	I1655F	probably damaging	Het
Cts3	A	G	13: 61,716,589 (GRCm39)	S16P	probably benign	Het
Cyp2c67	T	C	19: 39,604,084 (GRCm39)	Y424C	probably damaging	Het
Dip2c	T	C	13: 9,672,741 (GRCm39)		probably null	Het
Dnah5	T	C	15: 28,248,125 (GRCm39)		probably null	Het
Dpp4	A	G	2: 62,190,627 (GRCm39)		probably null	Het
Fam135b	T	G	15: 71,350,991 (GRCm39)	N295T	possibly damaging	Het
Fign	A	G	2: 63,810,916 (GRCm39)	V118A	probably benign	Het
Gpr108	A	T	17: 57,543,228 (GRCm39)	Y480*	probably null	Het
Ky	T	C	9: 102,419,469 (GRCm39)	V492A	probably benign	Het
Lmf1	G	A	17: 25,873,445 (GRCm39)	V317M	probably damaging	Het
Lrrc30	C	T	17: 67,939,472 (GRCm39)	G36E	probably damaging	Het
Map2	T	C	1: 66,452,466 (GRCm39)	V452A	probably benign	Het
Mks1	C	T	11: 87,747,666 (GRCm39)	T183M	possibly damaging	Het
Mpg	G	A	11: 32,179,517 (GRCm39)		probably null	Het
Nat10	A	G	2: 103,557,131 (GRCm39)	L841P	possibly damaging	Het
Nbeal1	A	G	1: 60,316,386 (GRCm39)	E1863G	probably benign	Het
Neurl1b	C	G	17: 26,657,720 (GRCm39)	H219Q	probably benign	Het
Nr2e3	T	A	9: 59,854,671 (GRCm39)	I292F	possibly damaging	Het
Nxn	T	C	11: 76,163,285 (GRCm39)	Y246C	probably damaging	Het
Or1o3	A	T	17: 37,573,964 (GRCm39)	M197K	probably benign	Het
Or4f4b	T	C	2: 111,313,823 (GRCm39)	F44S	probably damaging	Het
Or5ac15	T	G	16: 58,940,011 (GRCm39)	T141P	possibly damaging	Het
Or5h26	A	G	16: 58,988,080 (GRCm39)	V142A	probably benign	Het
Or8k17	A	T	2: 86,066,660 (GRCm39)	L166*	probably null	Het
Pcdha5	T	A	18: 37,093,544 (GRCm39)	F18I	probably benign	Het
Pcdhb17	A	G	18: 37,618,779 (GRCm39)	K190E	probably damaging	Het
Peg3	GTGGGGCTCCTGGCCATGGGGCTTATCATCATGGGGCTCCTGGCCATGGGGCTTATCATCATGGGGCTCCTGGCCATGGGGCTTATCATCATGGGGCTC	GTGGGGCTCCTGGCCATGGGGCTTATCATCATGGGGCTCCTGGCCATGGGGCTTATCATCATGGGGCTC	7: 6,712,167 (GRCm39)		probably benign	Het
Ppm1g	G	T	5: 31,362,447 (GRCm39)	Y284*	probably null	Het
Rp1	A	G	1: 4,218,054 (GRCm39)	V1026A	unknown	Het
Scap	C	T	9: 110,203,081 (GRCm39)	R252C	probably damaging	Het
Scn9a	C	A	2: 66,366,580 (GRCm39)	K734N	probably benign	Het
Sema5a	C	T	15: 32,682,471 (GRCm39)	S955F	probably damaging	Het
Serpinb10	A	G	1: 107,456,831 (GRCm39)		probably null	Het
Sfi1	ACA	ACATCTTCCCAAAGCCAGTCA	11: 3,103,382 (GRCm39)		probably benign	Het
Sh2d5	A	G	4: 137,986,467 (GRCm39)	T397A	probably benign	Het
Slc22a8	T	C	19: 8,587,409 (GRCm39)	F490L	probably benign	Het
Tbc1d19	A	T	5: 54,014,260 (GRCm39)	Y296F	probably damaging	Het
Tmppe	T	C	9: 114,233,862 (GRCm39)	S54P	possibly damaging	Het
Vmn1r123	A	T	7: 20,896,795 (GRCm39)	N229I	probably benign	Het
Wdr36	T	A	18: 32,987,624 (GRCm39)		probably null	Het
Wdr47	T	A	3: 108,550,480 (GRCm39)	M835K	possibly damaging	Het
Wscd2	A	T	5: 113,715,475 (GRCm39)	K438N	possibly damaging	Het
Xrcc6	T	A	15: 81,900,678 (GRCm39)		probably null	Het
Xrn1	T	A	9: 95,903,906 (GRCm39)	F1148I	possibly damaging	Het
Zmynd8	T	C	2: 165,654,346 (GRCm39)	D722G	probably 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
R6223:Col10a1	UTSW	10	34,271,183 (GRCm39)	missense	probably damaging	1.00
R7019:Col10a1	UTSW	10	34,270,947 (GRCm39)	missense	probably damaging	0.96
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'- AGCAACTAAGGGCCTCAATGG -3'
(R):5'- TACAGGCCTACCCAAACGTG -3'

Sequencing Primer
(F):5'- TCAATGGGCCCACTGGTC -3'
(R):5'- CCTTTCACATGCACGTGGTAGG -3'

Posted On

2019-10-24