Mutagenetix > Incidental Mutation

Incidental Mutation 'R5433:Col10a1'

428163

Institutional Source

Beutler Lab

Gene Symbol

Col10a1

Ensembl Gene

ENSMUSG00000039462

Gene Name

collagen, type X, alpha 1

Synonyms

Col10, Col10a-1

MMRRC Submission

042998-MU

Accession Numbers

Essential gene?

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

Stock #

R5433 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

34265977-34273081 bp(+) (GRCm39)

Type of Mutation

intron

DNA Base Change (assembly)

A to G at 34266735 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000150127 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000047885] [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

unknown
Transcript: ENSMUST00000105511
AA Change: T40A

SMART Domains

Protein: ENSMUSP00000101150
Gene: ENSMUSG00000039462
AA Change: T40A

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

0.2041

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.4%
20x: 95.8%

Validation Efficiency

100% (58/58)

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: 53 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700019D03Rik	T	C	1: 52,964,657 (GRCm39)	S24G	probably damaging	Het
1810064F22Rik	A	G	9: 22,119,039 (GRCm39)		noncoding transcript	Het
Aacs	A	T	5: 125,592,078 (GRCm39)	M589L	probably benign	Het
Adamts8	A	C	9: 30,873,012 (GRCm39)	H739P	probably benign	Het
Atp8b2	T	C	3: 89,860,216 (GRCm39)		probably benign	Het
BC030500	A	G	8: 59,366,043 (GRCm39)		probably benign	Het
Btnl9	T	A	11: 49,066,830 (GRCm39)		probably benign	Het
Cd74	G	T	18: 60,940,993 (GRCm39)	A31S	probably benign	Het
Ceacam3	G	A	7: 16,893,808 (GRCm39)	A440T	possibly damaging	Het
Ces1d	G	A	8: 93,912,664 (GRCm39)	T258I	probably benign	Het
Coro1b	C	T	19: 4,203,449 (GRCm39)	A430V	probably benign	Het
Cyp2c65	A	T	19: 39,081,928 (GRCm39)	I485L	probably benign	Het
Dio1	A	T	4: 107,163,977 (GRCm39)		probably benign	Het
Dmxl1	G	A	18: 50,000,966 (GRCm39)		probably null	Het
Dynlt5	A	G	4: 102,859,700 (GRCm39)	E84G	possibly damaging	Het
Elp6	A	G	9: 110,144,851 (GRCm39)	Y136C	probably damaging	Het
Gon4l	A	T	3: 88,803,532 (GRCm39)	Q1382L	possibly damaging	Het
Guca1a	T	C	17: 47,711,295 (GRCm39)	E17G	probably damaging	Het
Gucy2d	G	A	7: 98,098,982 (GRCm39)	G267E	probably damaging	Het
Gvin3	T	A	7: 106,199,314 (GRCm39)		noncoding transcript	Het
Hspg2	T	A	4: 137,256,105 (GRCm39)		probably null	Het
Il1a	G	T	2: 129,149,821 (GRCm39)	D26E	possibly damaging	Het
Il22b	T	A	10: 118,130,789 (GRCm39)	I36F	probably damaging	Het
Kcna1	A	T	6: 126,620,075 (GRCm39)	F82I	probably damaging	Het
Klhl18	G	C	9: 110,265,195 (GRCm39)	N335K	possibly damaging	Het
Lamtor5	T	G	3: 107,189,323 (GRCm39)	C120G	probably benign	Het
Lars1	A	G	18: 42,384,363 (GRCm39)	C72R	possibly damaging	Het
Lrrfip1	T	G	1: 91,014,848 (GRCm39)		probably null	Het
Mapkapk3	T	C	9: 107,133,491 (GRCm39)	D349G	probably damaging	Het
Mknk2	A	T	10: 80,503,059 (GRCm39)	I421N	probably benign	Het
Myh6	A	G	14: 55,191,381 (GRCm39)	I820T	probably benign	Het
Notch2	T	G	3: 98,033,450 (GRCm39)	V1182G	probably damaging	Het
Or1af1	T	G	2: 37,109,684 (GRCm39)	F61C	probably damaging	Het
Or1e16	AGCGGTCGTAGGC	AGC	11: 73,286,480 (GRCm39)		probably null	Het
Or2z2	C	T	11: 58,346,680 (GRCm39)	V32M	probably damaging	Het
Ppfia4	A	T	1: 134,245,632 (GRCm39)	S641T	probably damaging	Het
Prok1	T	A	3: 107,146,949 (GRCm39)	H6L	probably benign	Het
Ptprm	A	T	17: 67,000,468 (GRCm39)	V1172E	probably damaging	Het
Rasal3	C	T	17: 32,612,575 (GRCm39)	R762Q	probably benign	Het
Rgs20	G	T	1: 5,140,333 (GRCm39)	A23E	possibly damaging	Het
Rprd1a	T	C	18: 24,640,288 (GRCm39)	T163A	probably benign	Het
Rrm1	A	T	7: 102,114,974 (GRCm39)	N37I	probably damaging	Het
Shc4	T	A	2: 125,481,350 (GRCm39)	E520V	probably damaging	Het
Slc14a2	G	T	18: 78,252,143 (GRCm39)	P56Q	probably damaging	Het
Slc22a3	C	T	17: 12,677,377 (GRCm39)	G264S	probably damaging	Het
Svil	A	G	18: 5,059,294 (GRCm39)	E770G	probably damaging	Het
Svop	A	G	5: 114,198,186 (GRCm39)	V129A	probably damaging	Het
Szt2	A	T	4: 118,232,663 (GRCm39)		probably benign	Het
Tcof1	T	C	18: 60,951,105 (GRCm39)		probably benign	Het
Tmem30a	T	A	9: 79,687,930 (GRCm39)	I80F	probably damaging	Het
Vmn2r16	G	T	5: 109,511,708 (GRCm39)	L638F	probably damaging	Het
Xkr7	T	A	2: 152,896,244 (GRCm39)	I366N	probably damaging	Het
Zer1	A	G	2: 29,990,998 (GRCm39)		probably benign	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
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
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'- ACAGATCAGTGATGGGCTATGTG -3'
(R):5'- GGGTATTATGTTCCTATACTGACCTG -3'

Sequencing Primer
(F):5'- GCTATGTGTAATGATTCTCTTCTGC -3'
(R):5'- ATGCATCATTCCGCTGTACTAG -3'

Posted On

2016-09-01