Mutagenetix > Incidental Mutation

Incidental Mutation 'R9719:Col18a1'

730673

Institutional Source

Beutler Lab

Gene Symbol

Col18a1

Ensembl Gene

ENSMUSG00000001435

Gene Name

collagen, type XVIII, alpha 1

Synonyms

endostatin

MMRRC Submission

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9719 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

76888013-77002351 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 76949432 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Asparagine at position 27 (D27N)

Ref Sequence

ENSEMBL: ENSMUSP00000101049 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000072755] [ENSMUST00000081654] [ENSMUST00000105409]

AlphaFold

no structure available at present

Predicted Effect

unknown
Transcript: ENSMUST00000072755
AA Change: D27N

SMART Domains

Protein: ENSMUSP00000072538
Gene: ENSMUSG00000001435
AA Change: D27N

Domain	Start	End	E-Value	Type
Pfam:DUF959	16	218	6.8e-104	PFAM
low complexity region	295	307	N/A	INTRINSIC
FRI	369	484	4.03e-47	SMART
TSPN	492	680	4.25e-72	SMART
LamG	541	679	2.17e-2	SMART
low complexity region	699	715	N/A	INTRINSIC
low complexity region	719	734	N/A	INTRINSIC
low complexity region	739	751	N/A	INTRINSIC
Pfam:Collagen	820	881	5.5e-11	PFAM
low complexity region	921	942	N/A	INTRINSIC
Pfam:Collagen	951	1008	6.1e-10	PFAM
Pfam:Collagen	988	1053	1.4e-8	PFAM
Pfam:Collagen	1060	1117	7.3e-10	PFAM
low complexity region	1132	1147	N/A	INTRINSIC
low complexity region	1166	1181	N/A	INTRINSIC
low complexity region	1186	1202	N/A	INTRINSIC
Pfam:Collagen	1207	1267	8.2e-10	PFAM
low complexity region	1275	1288	N/A	INTRINSIC
low complexity region	1301	1319	N/A	INTRINSIC
low complexity region	1358	1393	N/A	INTRINSIC
low complexity region	1397	1414	N/A	INTRINSIC
low complexity region	1417	1433	N/A	INTRINSIC
low complexity region	1441	1454	N/A	INTRINSIC
Pfam:Endostatin	1461	1769	4.4e-116	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000081654

SMART Domains

Protein: ENSMUSP00000080358
Gene: ENSMUSG00000001435

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
TSPN	33	221	4.25e-72	SMART
LamG	82	220	2.17e-2	SMART
low complexity region	240	256	N/A	INTRINSIC
low complexity region	260	275	N/A	INTRINSIC
low complexity region	280	292	N/A	INTRINSIC
Pfam:Collagen	359	422	1.6e-10	PFAM
low complexity region	462	483	N/A	INTRINSIC
Pfam:Collagen	492	549	1.6e-9	PFAM
Pfam:Collagen	529	594	3.3e-8	PFAM
Pfam:Collagen	601	658	1.9e-9	PFAM
Pfam:Collagen	631	689	4e-8	PFAM
Pfam:Collagen	701	752	1.7e-7	PFAM
Pfam:Collagen	748	808	2.2e-9	PFAM
low complexity region	816	829	N/A	INTRINSIC
low complexity region	842	860	N/A	INTRINSIC
low complexity region	899	934	N/A	INTRINSIC
low complexity region	938	955	N/A	INTRINSIC
low complexity region	958	974	N/A	INTRINSIC
low complexity region	982	995	N/A	INTRINSIC
Pfam:Endostatin	999	1315	8.2e-151	PFAM

Predicted Effect

unknown
Transcript: ENSMUST00000105409
AA Change: D27N

SMART Domains

Protein: ENSMUSP00000101049
Gene: ENSMUSG00000001435
AA Change: D27N

Domain	Start	End	E-Value	Type
Pfam:DUF959	16	219	3.6e-100	PFAM
TSPN	245	433	4.25e-72	SMART
LamG	294	432	2.17e-2	SMART
low complexity region	452	468	N/A	INTRINSIC
low complexity region	472	487	N/A	INTRINSIC
low complexity region	492	504	N/A	INTRINSIC
low complexity region	542	613	N/A	INTRINSIC
low complexity region	630	648	N/A	INTRINSIC
low complexity region	674	695	N/A	INTRINSIC
Pfam:Collagen	700	761	5.4e-9	PFAM
Pfam:Collagen	741	806	4e-8	PFAM
Pfam:Collagen	813	874	2.1e-10	PFAM
Pfam:Collagen	846	901	1.2e-7	PFAM
Pfam:Collagen	913	964	2.1e-7	PFAM
Pfam:Collagen	960	1020	2.6e-9	PFAM
low complexity region	1028	1041	N/A	INTRINSIC
low complexity region	1054	1072	N/A	INTRINSIC
low complexity region	1111	1146	N/A	INTRINSIC
low complexity region	1150	1167	N/A	INTRINSIC
low complexity region	1170	1186	N/A	INTRINSIC
low complexity region	1194	1207	N/A	INTRINSIC
Pfam:Endostatin	1211	1527	1.1e-150	PFAM

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

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 XVIII collagen. This collagen is one of the multiplexins, extracellular matrix proteins that contain multiple triple-helix domains (collagenous domains) interrupted by non-collagenous domains. A long isoform of the protein has an N-terminal domain that is homologous to the extracellular part of frizzled receptors. Proteolytic processing at several endogenous cleavage sites in the C-terminal domain results in production of endostatin, a potent antiangiogenic protein that is able to inhibit angiogenesis and tumor growth. Mutations in this gene are associated with Knobloch syndrome. The main features of this syndrome involve retinal abnormalities, so type XVIII collagen may play an important role in retinal structure and in neural tube closure. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit defects in hyaloid vessel regression, attenuated visual function, abnormal electroretinograms, broad proximal tubule basement membrane, podocyte effacement, and softened glomeruli. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 48 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Alppl2	T	A	1: 87,016,136 (GRCm39)	Q241L	probably benign	Het
Apob	T	A	12: 8,065,464 (GRCm39)	N4144K	probably benign	Het
B4gat1	A	G	19: 5,090,516 (GRCm39)	H413R	probably benign	Het
Ccdc179	T	C	7: 51,664,612 (GRCm39)	T28A	probably benign	Het
Ceacam5	A	C	7: 17,491,835 (GRCm39)	D735A	probably damaging	Het
Colgalt1	A	G	8: 72,073,456 (GRCm39)	E359G	probably benign	Het
Crybg2	T	A	4: 133,793,148 (GRCm39)	I261N	probably benign	Het
Cyyr1	A	T	16: 85,219,203 (GRCm39)	L68Q	unknown	Het
Dgkz	T	A	2: 91,768,911 (GRCm39)		probably null	Het
Efcab3	A	T	11: 104,867,912 (GRCm39)	E3947V	unknown	Het
Eif2ak2	C	A	17: 79,162,783 (GRCm39)	D472Y	probably damaging	Het
Elp2	A	G	18: 24,755,539 (GRCm39)	T429A	possibly damaging	Het
Fen1	G	A	19: 10,178,016 (GRCm39)	H143Y	probably benign	Het
Gm10518	C	A	1: 179,631,113 (GRCm39)	R58S	unknown	Het
Hspa1b	T	C	17: 35,176,467 (GRCm39)	D506G	probably damaging	Het
Inhca	G	T	9: 103,132,014 (GRCm39)	P569H	probably benign	Het
Kcna7	A	G	7: 45,056,390 (GRCm39)	D202G	probably benign	Het
Krt9	TCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCC	TCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCC	11: 100,079,903 (GRCm39)		probably benign	Het
Mal	C	T	2: 127,498,025 (GRCm39)	S10N	possibly damaging	Het
Mgat2	T	A	12: 69,232,115 (GRCm39)	W230R	probably damaging	Het
Myo3a	A	T	2: 22,436,493 (GRCm39)	T883S	probably benign	Het
Ncaph2	T	C	15: 89,249,526 (GRCm39)	S277P	probably benign	Het
Olfm3	G	A	3: 114,916,091 (GRCm39)	W341*	probably null	Het
Or13c7e-ps1	A	C	4: 43,781,454 (GRCm39)	M292R	probably damaging	Het
Or1p1	A	C	11: 74,180,146 (GRCm39)	I225L	probably damaging	Het
Or5b119	A	G	19: 13,457,368 (GRCm39)	S65P	probably damaging	Het
Or5d46	T	A	2: 88,169,928 (GRCm39)	N6K		Het
Or5g26	T	A	2: 85,494,608 (GRCm39)	I57F	probably benign	Het
Or6z1	C	A	7: 6,504,999 (GRCm39)	M75I	probably benign	Het
Pcnx4	T	C	12: 72,603,039 (GRCm39)	Y434H	probably damaging	Het
Ptpn14	T	A	1: 189,583,484 (GRCm39)	M777K	probably benign	Het
Rasef	A	G	4: 73,688,102 (GRCm39)	I17T	possibly damaging	Het
Rptor	A	T	11: 119,781,940 (GRCm39)	D1089V	probably benign	Het
Scel	A	T	14: 103,809,442 (GRCm39)		probably null	Het
Scfd2	A	T	5: 74,386,004 (GRCm39)	L605Q	probably damaging	Het
Son	A	G	16: 91,456,440 (GRCm39)	E1729G	probably damaging	Het
Spata31e2	C	G	1: 26,722,820 (GRCm39)	E787Q	probably benign	Het
Spout1	A	G	2: 30,065,813 (GRCm39)	Y243H	probably benign	Het
Syne1	A	G	10: 5,276,601 (GRCm39)	F1765S	possibly damaging	Het
Tet2	A	T	3: 133,191,803 (GRCm39)	V877E	possibly damaging	Het
Txn2	T	C	15: 77,812,289 (GRCm39)		probably benign	Het
Vmn1r158	T	C	7: 22,489,331 (GRCm39)	I293V	possibly damaging	Het
Vmn1r81	G	A	7: 11,994,449 (GRCm39)	T53I	probably damaging	Het
Vps18	T	C	2: 119,127,553 (GRCm39)	F792S	probably damaging	Het
Vps25	A	G	11: 101,146,853 (GRCm39)	D91G	probably null	Het
Wdr26	G	A	1: 181,015,224 (GRCm39)	L396F	possibly damaging	Het
Zfp1005	T	A	2: 150,111,304 (GRCm39)	C665S	possibly damaging	Het
Zfp26	T	C	9: 20,347,861 (GRCm39)	E901G	possibly damaging	Het

Other mutations in Col18a1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00952:Col18a1	APN	10	76,905,813 (GRCm39)	missense	possibly damaging	0.93
IGL01023:Col18a1	APN	10	76,906,809 (GRCm39)	missense	probably damaging	0.98
IGL01304:Col18a1	APN	10	76,911,975 (GRCm39)	unclassified	probably benign
IGL01519:Col18a1	APN	10	76,895,157 (GRCm39)	missense	probably damaging	0.99
IGL02217:Col18a1	APN	10	76,889,132 (GRCm39)	missense	probably damaging	0.96
IGL02275:Col18a1	APN	10	76,895,217 (GRCm39)	missense	possibly damaging	0.92
IGL02283:Col18a1	APN	10	76,948,943 (GRCm39)	missense	possibly damaging	0.71
IGL02492:Col18a1	APN	10	76,907,855 (GRCm39)	splice site	probably benign
IGL02673:Col18a1	APN	10	76,894,997 (GRCm39)	missense	probably damaging	1.00
IGL02710:Col18a1	APN	10	76,949,146 (GRCm39)	missense	possibly damaging	0.92
IGL02850:Col18a1	APN	10	76,932,300 (GRCm39)	missense	probably damaging	0.98
IGL03085:Col18a1	APN	10	76,895,015 (GRCm39)	splice site	probably benign
IGL03102:Col18a1	APN	10	76,903,457 (GRCm39)	splice site	probably benign
IGL03139:Col18a1	APN	10	76,949,177 (GRCm39)	missense	possibly damaging	0.84
IGL03181:Col18a1	APN	10	76,891,532 (GRCm39)	missense	probably damaging	1.00
IGL03183:Col18a1	APN	10	76,909,588 (GRCm39)	missense	probably damaging	1.00
R0039:Col18a1	UTSW	10	76,913,002 (GRCm39)	missense	probably damaging	1.00
R0180:Col18a1	UTSW	10	76,932,351 (GRCm39)	missense	probably benign	0.33
R0225:Col18a1	UTSW	10	76,924,748 (GRCm39)	missense	possibly damaging	0.90
R0335:Col18a1	UTSW	10	76,895,197 (GRCm39)	missense	probably damaging	0.99
R0336:Col18a1	UTSW	10	76,894,570 (GRCm39)	missense	probably damaging	1.00
R1471:Col18a1	UTSW	10	76,932,040 (GRCm39)	missense	unknown
R1538:Col18a1	UTSW	10	76,907,170 (GRCm39)	missense	probably damaging	1.00
R1594:Col18a1	UTSW	10	76,948,870 (GRCm39)	missense	possibly damaging	0.51
R1631:Col18a1	UTSW	10	76,895,131 (GRCm39)	missense	probably damaging	0.99
R1774:Col18a1	UTSW	10	76,895,815 (GRCm39)	missense	probably damaging	0.96
R1934:Col18a1	UTSW	10	76,948,578 (GRCm39)	missense	possibly damaging	0.73
R1990:Col18a1	UTSW	10	76,916,988 (GRCm39)	missense	unknown
R1991:Col18a1	UTSW	10	76,916,988 (GRCm39)	missense	unknown
R1992:Col18a1	UTSW	10	76,916,988 (GRCm39)	missense	unknown
R2081:Col18a1	UTSW	10	76,890,019 (GRCm39)	missense	probably damaging	1.00
R2082:Col18a1	UTSW	10	76,895,127 (GRCm39)	missense	probably damaging	1.00
R2351:Col18a1	UTSW	10	76,948,538 (GRCm39)	missense	probably benign	0.00
R2510:Col18a1	UTSW	10	76,932,102 (GRCm39)	missense	unknown
R3076:Col18a1	UTSW	10	76,924,762 (GRCm39)	missense	possibly damaging	0.57
R3433:Col18a1	UTSW	10	76,932,102 (GRCm39)	missense	unknown
R3800:Col18a1	UTSW	10	76,903,221 (GRCm39)	nonsense	probably null
R3918:Col18a1	UTSW	10	76,889,192 (GRCm39)	missense	probably benign	0.05
R3981:Col18a1	UTSW	10	76,924,721 (GRCm39)	missense	probably damaging	0.99
R3983:Col18a1	UTSW	10	76,924,721 (GRCm39)	missense	probably damaging	0.99
R4182:Col18a1	UTSW	10	76,894,675 (GRCm39)	splice site	probably null
R4239:Col18a1	UTSW	10	76,932,001 (GRCm39)	missense	unknown
R5014:Col18a1	UTSW	10	76,906,794 (GRCm39)	critical splice donor site	probably null
R5107:Col18a1	UTSW	10	76,913,057 (GRCm39)	critical splice acceptor site	probably null
R5413:Col18a1	UTSW	10	76,905,310 (GRCm39)	missense	probably damaging	1.00
R5503:Col18a1	UTSW	10	76,907,454 (GRCm39)	missense	probably damaging	1.00
R5524:Col18a1	UTSW	10	76,894,558 (GRCm39)	missense	probably damaging	1.00
R5772:Col18a1	UTSW	10	77,002,177 (GRCm39)	missense	unknown
R5958:Col18a1	UTSW	10	76,932,231 (GRCm39)	missense	probably benign	0.01
R6280:Col18a1	UTSW	10	76,948,323 (GRCm39)	intron	probably benign
R6309:Col18a1	UTSW	10	76,948,576 (GRCm39)	intron	probably benign
R6603:Col18a1	UTSW	10	76,899,811 (GRCm39)	critical splice donor site	probably null
R6608:Col18a1	UTSW	10	76,948,628 (GRCm39)	intron	probably benign
R6805:Col18a1	UTSW	10	76,890,073 (GRCm39)	missense	probably damaging	1.00
R6890:Col18a1	UTSW	10	76,949,318 (GRCm39)	intron	probably benign
R6938:Col18a1	UTSW	10	76,948,333 (GRCm39)	intron	probably benign
R7002:Col18a1	UTSW	10	77,002,177 (GRCm39)	missense	unknown
R7154:Col18a1	UTSW	10	76,908,799 (GRCm39)	missense	probably benign	0.25
R7204:Col18a1	UTSW	10	76,921,110 (GRCm39)	missense	unknown
R7278:Col18a1	UTSW	10	76,932,118 (GRCm39)	missense	unknown
R7442:Col18a1	UTSW	10	76,932,072 (GRCm39)	missense	unknown
R7453:Col18a1	UTSW	10	76,921,044 (GRCm39)	splice site	probably null
R7597:Col18a1	UTSW	10	76,949,137 (GRCm39)	missense	unknown
R7615:Col18a1	UTSW	10	76,902,839 (GRCm39)	missense	probably damaging	1.00
R7671:Col18a1	UTSW	10	76,921,217 (GRCm39)	missense	unknown
R7696:Col18a1	UTSW	10	76,921,106 (GRCm39)	missense	unknown
R7719:Col18a1	UTSW	10	76,913,846 (GRCm39)	missense	probably benign	0.13
R7772:Col18a1	UTSW	10	76,904,220 (GRCm39)	splice site	probably null
R8077:Col18a1	UTSW	10	76,916,685 (GRCm39)	missense	unknown
R8085:Col18a1	UTSW	10	76,924,741 (GRCm39)	missense	unknown
R8097:Col18a1	UTSW	10	76,948,342 (GRCm39)	missense	unknown
R8117:Col18a1	UTSW	10	76,895,808 (GRCm39)	missense	probably benign	0.41
R8130:Col18a1	UTSW	10	76,910,284 (GRCm39)	missense	probably benign	0.03
R8151:Col18a1	UTSW	10	76,948,418 (GRCm39)	missense	unknown
R8379:Col18a1	UTSW	10	76,889,072 (GRCm39)	missense	probably benign	0.08
R8479:Col18a1	UTSW	10	76,916,988 (GRCm39)	missense	unknown
R8523:Col18a1	UTSW	10	76,890,068 (GRCm39)	missense	probably damaging	0.99
R8862:Col18a1	UTSW	10	76,949,044 (GRCm39)	nonsense	probably null
R9109:Col18a1	UTSW	10	76,893,204 (GRCm39)	missense	probably damaging	1.00
R9298:Col18a1	UTSW	10	76,893,204 (GRCm39)	missense	probably damaging	1.00
R9312:Col18a1	UTSW	10	76,894,606 (GRCm39)	missense	probably damaging	0.98
R9366:Col18a1	UTSW	10	76,932,258 (GRCm39)	missense	unknown
R9399:Col18a1	UTSW	10	76,916,584 (GRCm39)	missense	unknown
R9559:Col18a1	UTSW	10	76,913,630 (GRCm39)	missense	probably damaging	1.00
R9649:Col18a1	UTSW	10	76,916,673 (GRCm39)	missense	unknown
R9689:Col18a1	UTSW	10	76,916,578 (GRCm39)	nonsense	probably null
Z1176:Col18a1	UTSW	10	76,948,685 (GRCm39)	missense	unknown
Z1176:Col18a1	UTSW	10	76,891,543 (GRCm39)	missense	possibly damaging	0.81
Z1177:Col18a1	UTSW	10	76,948,672 (GRCm39)	missense	unknown

Predicted Primers

PCR Primer
(F):5'- CAGAATCTTGGCTCCAACGC -3'
(R):5'- TCTCAGGCTGGGTTCATTCC -3'

Sequencing Primer
(F):5'- CTTCATGTCTGGGCTCGCAG -3'
(R):5'- ATTCCCTTCTGCCAGAGGGAAG -3'

Posted On

2022-10-06