Mutagenetix > Incidental Mutation

Incidental Mutation 'R7019:Col10a1'

545516

Institutional Source

Beutler Lab

Gene Symbol

Col10a1

Ensembl Gene

ENSMUSG00000039462

Gene Name

collagen, type X, alpha 1

Synonyms

Col10, Col10a-1

MMRRC Submission

045120-MU

Accession Numbers

Essential gene?

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

Stock #

R7019 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

34265977-34273081 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 34270947 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Phenylalanine at position 306 (L306F)

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: L306F

PolyPhen 2 Score 0.961 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000101150
Gene: ENSMUSG00000039462
AA Change: L306F

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: 99.9%
10x: 99.6%
20x: 98.7%

Validation Efficiency

100% (61/61)

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: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abat	A	T	16: 8,436,395 (GRCm39)	K414*	probably null	Het
Aco1	T	A	4: 40,186,376 (GRCm39)	I596N	probably damaging	Het
Adgre1	A	C	17: 57,717,945 (GRCm39)	D319A	probably damaging	Het
Birc6	T	C	17: 74,916,340 (GRCm39)	V445A	probably benign	Het
Btd	A	C	14: 31,389,062 (GRCm39)	Q261P	probably damaging	Het
Btd	G	T	14: 31,389,063 (GRCm39)	Q261H	possibly damaging	Het
C7	T	A	15: 5,075,164 (GRCm39)	Y176F	probably benign	Het
Ccdc102a	T	C	8: 95,636,431 (GRCm39)	S287G	probably benign	Het
Ccdc178	T	A	18: 22,283,495 (GRCm39)	T12S	probably benign	Het
Cnga4	G	T	7: 105,055,036 (GRCm39)	A104S	probably benign	Het
Cpne5	T	C	17: 29,445,196 (GRCm39)	D36G	probably damaging	Het
Csmd2	G	A	4: 128,262,856 (GRCm39)	D681N		Het
Cspg4b	C	T	13: 113,488,284 (GRCm39)	T102I	probably benign	Het
Cstl1	A	G	2: 148,597,223 (GRCm39)	M75V	probably benign	Het
Cyp26a1	T	C	19: 37,687,260 (GRCm39)	L149P	probably damaging	Het
D630045J12Rik	T	G	6: 38,171,570 (GRCm39)	E866A	probably benign	Het
Dlec1	C	T	9: 118,941,490 (GRCm39)	P292L	probably benign	Het
Dpp3	T	G	19: 4,966,817 (GRCm39)	E402A	possibly damaging	Het
Egf	T	C	3: 129,511,713 (GRCm39)		probably null	Het
Epha5	T	C	5: 84,564,321 (GRCm39)	Q15R	possibly damaging	Het
Esyt3	A	G	9: 99,197,338 (GRCm39)	F831L	probably benign	Het
Fam50b	G	A	13: 34,931,084 (GRCm39)	E187K	possibly damaging	Het
Fut7	A	G	2: 25,315,792 (GRCm39)	D350G	probably benign	Het
Gab1	C	A	8: 81,511,446 (GRCm39)	E466D	probably damaging	Het
Glrp1	A	T	1: 88,430,890 (GRCm39)	M160K	unknown	Het
Gngt1	T	C	6: 3,994,088 (GRCm39)		probably null	Het
Gprc6a	A	T	10: 51,507,508 (GRCm39)	V7E	possibly damaging	Het
Idh3b	A	T	2: 130,122,886 (GRCm39)	V301D	probably damaging	Het
Ifi202b	A	C	1: 173,791,524 (GRCm39)	C385G	probably benign	Het
Ilvbl	T	A	10: 78,414,920 (GRCm39)	L261Q	probably damaging	Het
Irx6	T	A	8: 93,405,362 (GRCm39)	L410Q	probably damaging	Het
Ism2	T	C	12: 87,346,437 (GRCm39)	M15V	unknown	Het
Itih5	C	A	2: 10,195,138 (GRCm39)	R177S	probably damaging	Het
Klra3	C	T	6: 130,304,087 (GRCm39)	G202R	probably damaging	Het
Krt7	T	C	15: 101,311,851 (GRCm39)	V103A	probably damaging	Het
Lama3	T	C	18: 12,661,475 (GRCm39)	S2145P	probably damaging	Het
Mlph	A	G	1: 90,869,428 (GRCm39)	R477G	probably damaging	Het
Mybpc1	T	A	10: 88,379,581 (GRCm39)	L653F	probably damaging	Het
Myrfl	A	G	10: 116,617,852 (GRCm39)		probably null	Het
Myrip	T	G	9: 120,251,573 (GRCm39)	L232R	probably damaging	Het
Nrdc	A	T	4: 108,885,999 (GRCm39)	H126L	probably benign	Het
Or4n5	A	T	14: 50,133,124 (GRCm39)	I45N	probably damaging	Het
Or5p50	G	T	7: 107,422,365 (GRCm39)	L104I	probably benign	Het
Or8c11	T	A	9: 38,290,098 (GRCm39)	L307Q	possibly damaging	Het
Pcdhb10	T	A	18: 37,546,056 (GRCm39)	N377K	probably damaging	Het
Pigt	CCAGGCCAGTGAGTAGGTTTGTCTCTGTCTAGTGTGGATCTGTAACCACAGGCCAGTGAGTAGGTTTGTCTCTGTCTAGTGTGGATCTGTAACCACAGGCCAGTGAGTAGGTTTGTCTCTGTCTAGTGTGGAT	CCAGGCCAGTGAGTAGGTTTGTCTCTGTCTAGTGTGGATCTGTAACCACAGGCCAGTGAGTAGGTTTGTCTCTGTCTAGTGTGGAT	2: 164,341,589 (GRCm39)		probably null	Het
Prkdc	A	C	16: 15,587,830 (GRCm39)	I2572L	probably benign	Het
Ptpro	C	A	6: 137,357,476 (GRCm39)	D322E	probably benign	Het
R3hcc1	A	G	14: 69,941,574 (GRCm39)	I332T	probably damaging	Het
Rab8a	T	C	8: 72,915,227 (GRCm39)	F9L	probably damaging	Het
Ranbp3l	A	T	15: 9,057,241 (GRCm39)	K165N	probably damaging	Het
Rock2	T	A	12: 17,027,741 (GRCm39)	C1353S	probably damaging	Het
Rsad2	T	A	12: 26,506,418 (GRCm39)	M1L	possibly damaging	Het
Tymp	A	T	15: 89,260,484 (GRCm39)		probably null	Het
Vmn1r104	A	G	7: 20,268,491 (GRCm39)	M244V	probably benign	Het
Vmn1r232	G	A	17: 21,133,547 (GRCm39)	T351M	possibly damaging	Het
Vmn2r50	A	G	7: 9,784,172 (GRCm39)	Y101H	probably benign	Het
Vmn2r57	A	G	7: 41,078,089 (GRCm39)	L123P	probably damaging	Het
Wdr17	T	C	8: 55,134,488 (GRCm39)	N331D	probably damaging	Het
Wdr47	C	T	3: 108,521,671 (GRCm39)	Q89*	probably null	Het
Zcchc4	A	T	5: 52,941,375 (GRCm39)	T57S	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
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
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'- TCAAAGGTGACCGGGGTTTC -3'
(R):5'- AGACCTATCTCACCTTTAGCGC -3'

Sequencing Primer
(F):5'- ATCAGGTCCACCAGGTCC -3'
(R):5'- ACCTTTAGCGCCTGGAATG -3'

Posted On

2019-05-13