Mutagenetix > Incidental Mutations

Incidental Mutation 'RF014:Col16a1'

603394

Institutional Source

Beutler Lab

Gene Symbol

Col16a1

Ensembl Gene

ENSMUSG00000040690

Gene Name

collagen, type XVI, alpha 1

Synonyms

2700007F12Rik, [a]1 (XVI) collagen, A530052M23Rik

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.100) question?

Stock #

RF014 (G1)

Quality Score

214.628

Status

Not validated

Chromosome

Chromosomal Location

130047840-130099283 bp(+) (GRCm38)

Type of Mutation

critical splice acceptor site

DNA Base Change (assembly)

TTTTT to TTTTTCTTTT at 130093067 bp

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000035802 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000044565] [ENSMUST00000143432] [ENSMUST00000143577]

Predicted Effect

probably benign
Transcript: ENSMUST00000044565

SMART Domains

Protein: ENSMUSP00000035802
Gene: ENSMUSG00000040690

Domain	Start	End	E-Value	Type
signal peptide	1	21	N/A	INTRINSIC
TSPN	50	231	1.07e-68	SMART
internal_repeat_4	330	355	2.35e-7	PROSPERO
Pfam:Collagen	372	431	1.6e-8	PFAM
low complexity region	441	507	N/A	INTRINSIC
low complexity region	525	542	N/A	INTRINSIC
internal_repeat_2	546	562	2.68e-9	PROSPERO
internal_repeat_1	547	580	9.92e-10	PROSPERO
Pfam:Collagen	584	646	1.5e-9	PFAM
internal_repeat_5	662	689	6.35e-7	PROSPERO
internal_repeat_3	662	731	1.96e-8	PROSPERO
internal_repeat_7	679	695	2.06e-5	PROSPERO
internal_repeat_6	682	730	7.63e-6	PROSPERO
internal_repeat_1	685	742	9.92e-10	PROSPERO
Pfam:Collagen	796	850	3.4e-9	PFAM
internal_repeat_5	859	889	6.35e-7	PROSPERO
low complexity region	891	922	N/A	INTRINSIC
low complexity region	990	1000	N/A	INTRINSIC
Pfam:Collagen	1001	1064	1.4e-10	PFAM
low complexity region	1090	1112	N/A	INTRINSIC
internal_repeat_7	1114	1130	2.06e-5	PROSPERO
low complexity region	1132	1162	N/A	INTRINSIC
low complexity region	1171	1222	N/A	INTRINSIC
low complexity region	1230	1282	N/A	INTRINSIC
internal_repeat_2	1283	1299	2.68e-9	PROSPERO
internal_repeat_6	1287	1335	7.63e-6	PROSPERO
Pfam:Collagen	1350	1411	1.8e-9	PFAM
Pfam:Collagen	1446	1503	5.3e-10	PFAM
low complexity region	1505	1525	N/A	INTRINSIC
low complexity region	1528	1549	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000143432

SMART Domains

Protein: ENSMUSP00000120384
Gene: ENSMUSG00000040690

Domain	Start	End	E-Value	Type
signal peptide	1	21	N/A	INTRINSIC
TSPN	50	231	1.07e-68	SMART
internal_repeat_1	330	353	5.41e-8	PROSPERO
Pfam:Collagen	372	426	2.1e-9	PFAM
low complexity region	441	507	N/A	INTRINSIC
low complexity region	525	542	N/A	INTRINSIC
internal_repeat_1	546	569	5.41e-8	PROSPERO
internal_repeat_2	547	580	5.41e-8	PROSPERO
Pfam:Collagen	584	646	2.7e-10	PFAM
Pfam:Collagen	659	736	8.6e-8	PFAM
Pfam:Collagen	745	797	1.6e-7	PFAM
Pfam:Collagen	796	850	5.9e-10	PFAM
Pfam:Collagen	848	923	1.6e-7	PFAM
low complexity region	974	984	N/A	INTRINSIC
Pfam:Collagen	987	1045	1e-11	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000143577

SMART Domains

Protein: ENSMUSP00000120339
Gene: ENSMUSG00000040690

Domain	Start	End	E-Value	Type
internal_repeat_7	1	43	5.7e-5	PROSPERO
Pfam:Collagen	57	112	2e-9	PFAM
low complexity region	126	192	N/A	INTRINSIC
low complexity region	210	227	N/A	INTRINSIC
internal_repeat_2	231	247	1.5e-10	PROSPERO
internal_repeat_1	232	265	5.16e-11	PROSPERO
Pfam:Collagen	269	331	3.4e-10	PFAM
Pfam:Collagen	360	421	7e-11	PFAM
Pfam:Collagen	430	482	1.9e-7	PFAM
Pfam:Collagen	481	535	7.8e-10	PFAM
Pfam:Collagen	560	623	1.4e-7	PFAM
internal_repeat_9	640	665	9.73e-5	PROSPERO
low complexity region	675	685	N/A	INTRINSIC
Pfam:Collagen	686	747	2.5e-11	PFAM
Pfam:Collagen	730	802	5.2e-9	PFAM
Pfam:Collagen	783	860	9.2e-9	PFAM
low complexity region	871	922	N/A	INTRINSIC
low complexity region	930	985	N/A	INTRINSIC
internal_repeat_2	986	1002	1.5e-10	PROSPERO
internal_repeat_5	990	1038	7.88e-7	PROSPERO
low complexity region	1041	1110	N/A	INTRINSIC
Pfam:Collagen	1149	1205	1.8e-10	PFAM
Pfam:Collagen	1203	1260	1.1e-7	PFAM

Coding Region Coverage

1x: 99.8%
3x: 99.7%
10x: 99.4%
20x: 98.6%

Validation Efficiency

98% (49/50)

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 XVI collagen, a member of the FACIT collagen family (fibril-associated collagens with interrupted helices). Members of this collagen family are found in association with fibril-forming collagens such as type I and II, and serve to maintain the integrity of the extracellular matrix. High levels of type XVI collagen have been found in fibroblasts and keratinocytes, and in smooth muscle and amnion. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5430401F13Rik	AGAAAGGAAAAGGTGGCCAGCAAAAACAGAAAGGAAAAGGTGGCCAG	AGAAAGGAAAAGGTGGCCAGCAAAAACAGAAAGGAAAAGGTGGCCAGCAAAAACAGAAAGGAAAAGGTGGCCAG	6: 131,552,857		probably benign	Het
9530003J23Rik	A	G	10: 117,234,417	*152Q	probably null	Het
A2ml1	T	C	6: 128,570,068	N366S	probably damaging	Het
Abca5	T	C	11: 110,279,754		probably null	Het
Acaca	T	C	11: 84,231,724	V323A	probably benign	Het
Agbl3	T	A	6: 34,799,358	D266E	possibly damaging	Het
Aggf1	A	T	13: 95,370,768	S170T	possibly damaging	Het
Amhr2	A	T	15: 102,453,154	S467C	probably benign	Het
Begain	GCCGCC	GCCGCCACCGCC	12: 109,033,422		probably benign	Het
Best3	A	T	10: 117,004,505	Q280L	probably damaging	Het
Calhm1	CTGTGGCTGTGG	CTGTGGCTGTGGGTGTGGCTGTGG	19: 47,141,265		probably benign	Het
Ccdc186	A	G	19: 56,813,472	L71S	probably benign	Het
Ces1d	C	A	8: 93,176,165		probably null	Het
Chga	AGC	AGCGGC	12: 102,561,393		probably benign	Het
Chga	AGC	AGCTGC	12: 102,561,405		probably benign	Het
Clstn3	T	A	6: 124,459,266	K212*	probably null	Het
Cpxm2	G	T	7: 132,070,863	T319K	possibly damaging	Het
Cyb5r4	TGCCCAGGGATGTGACAGACACAC	TGCCCAGGGATGTGACAGACACACCGCCCAGGGATGTGACAGACACAC	9: 87,040,415		probably benign	Het
Dst	T	C	1: 34,247,679	S3364P	probably benign	Het
Edc4	C	T	8: 105,884,600	T61M	probably benign	Het
Fndc5	A	G	4: 129,142,167	H199R	probably benign	Het
Gm43302	T	A	5: 105,274,757	I470F	possibly damaging	Het
Gne	G	T	4: 44,060,045	A147D	probably damaging	Het
Igkv12-89	G	GCAACGCCAC	6: 68,835,286		probably benign	Het
Irf9	C	T	14: 55,605,877	R179*	probably null	Het
Jakmip1	A	T	5: 37,174,526	K850M	possibly damaging	Het
Kalrn	G	A	16: 34,039,933	T1884I	probably benign	Het
Krtap28-10	CCACCACAGCCACAGCCACCACAGCCACAG	CCACCACAGCCACAGACACCACAGCCACAGCCACCACAGCCACAG	1: 83,042,251		probably benign	Het
Las1l	CTCCTCCTTCTCCTCTTCCTC	CTCCTC	X: 95,940,657		probably benign	Het
Lctl	A	G	9: 64,118,930	Y89C	probably damaging	Het
Lpgat1	GCC	GCCTCC	1: 191,718,553		probably benign	Het
Luzp2	A	T	7: 55,172,205	I157F	probably damaging	Het
Mamld1	GCA	GCACCA	X: 71,118,845		probably benign	Het
Map1a	GCTCCAGCTCCAGCTCCAGCTCCA	GCTCCAGCTCCAGCTCCAGCTCCAGCTCCACCTCCAGCTCCAGCTCCAGCTCCA	2: 121,306,295		probably benign	Het
Mbd3l1	A	T	9: 18,485,000	E140D	possibly damaging	Het
Mlh3	T	A	12: 85,268,029	Q461L	probably benign	Het
Mto1	G	T	9: 78,448,316	R7L	probably benign	Het
Muc4	A	T	16: 32,751,858	S579C	probably damaging	Het
Ngfr	T	C	11: 95,578,201	Y117C	probably damaging	Het
Olfr432	A	T	1: 174,050,987	I205F	possibly damaging	Het
Olfr537-ps1	A	T	7: 140,538,777	M87L	probably benign	Het
Olfr926	C	A	9: 38,877,900	H241Q	probably benign	Het
Plch2	A	G	4: 155,007,120	S179P	probably damaging	Het
Pogz	T	G	3: 94,878,247	S838A	possibly damaging	Het
Pot1b	T	A	17: 55,674,106	T303S	probably benign	Het
Pou2f2	T	A	7: 25,115,737	I72L	unknown	Het
Ppil2	C	T	16: 17,097,418	V109M	probably damaging	Het
Ptpn4	A	G	1: 119,684,465		probably null	Het
Ptprs	A	T	17: 56,416,935	I1686N	probably damaging	Het
Rfx4	CTCTCT	CTCTCTCTCTCTCTCTTTCTCT	10: 84,858,489		probably benign	Het
Rnf14	T	A	18: 38,309,570	V308E	probably damaging	Het
Setd1a	TGGTGGTGG	TGGTGGTGGGGGTGGTGG	7: 127,785,346		probably benign	Het
Sgo2b	T	C	8: 63,931,405	T186A	possibly damaging	Het
Six3	CGG	CGGTGG	17: 85,621,356		probably benign	Het
Six4	TG	T	12: 73,103,582		probably null	Het
Stox1	T	A	10: 62,664,246	H845L	probably benign	Het
Supt20	AGCAGC	AGCAGCGGCAGC	3: 54,727,665		probably benign	Het
Thegl	CAGCGATCCTCCCCAGTCCCGCA	CAGCGATCCTCCCCAGTCCCGCAGGGCGAGCGATCCTCCCCAGTCCCGCA	5: 77,016,400		probably benign	Het
Trappc9	A	AGCTGCTGCTGCTGCT	15: 72,801,283		probably benign	Het
Trim33	T	C	3: 103,329,092	V506A	possibly damaging	Het
Uckl1	T	C	2: 181,570,194	D373G	probably benign	Het
Vmn2r94	G	T	17: 18,253,287	C492*	probably null	Het
Wdr33	A	G	18: 31,881,273	D396G	probably damaging	Het
Zbtb11	A	T	16: 55,980,597	I105L	probably damaging	Het
Zbtb40	A	T	4: 137,017,306	C268S	probably benign	Het
Zfp36l1	T	A	12: 80,109,744	M288L	probably benign	Het
Zfp384	CC	CCAAGGCCCAGGAC	6: 125,036,466		probably benign	Het
Zfp72	A	G	13: 74,375,054	F15S	probably benign	Het
Znrd1as	CACCACCACCAC	CACCACCACCACCACCACCACGACCACCACCAC	17: 36,965,060		probably benign	Het

Other mutations in Col16a1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00501:Col16a1	APN	4	130094552	splice site	probably null
IGL00885:Col16a1	APN	4	130096910	missense	probably damaging	1.00
IGL01931:Col16a1	APN	4	130072841	missense	possibly damaging	0.47
IGL02142:Col16a1	APN	4	130051647	splice site	probably null
IGL02307:Col16a1	APN	4	130059009	missense	probably damaging	1.00
IGL02731:Col16a1	APN	4	130053530	unclassified	probably benign
IGL02742:Col16a1	APN	4	130061379	unclassified	probably benign
PIT4520001:Col16a1	UTSW	4	130051663	missense	unknown
R0127:Col16a1	UTSW	4	130052857	missense	probably damaging	1.00
R0131:Col16a1	UTSW	4	130067096	missense	unknown
R0131:Col16a1	UTSW	4	130067096	missense	unknown
R0132:Col16a1	UTSW	4	130067096	missense	unknown
R0299:Col16a1	UTSW	4	130058318	frame shift	probably null
R0355:Col16a1	UTSW	4	130058413	splice site	probably benign
R0395:Col16a1	UTSW	4	130073109	missense	probably damaging	1.00
R0485:Col16a1	UTSW	4	130090497	splice site	probably benign
R0573:Col16a1	UTSW	4	130068475	splice site	probably benign
R1274:Col16a1	UTSW	4	130097801	missense	probably damaging	0.98
R1619:Col16a1	UTSW	4	130098940	missense	probably damaging	1.00
R1759:Col16a1	UTSW	4	130084269	missense	probably damaging	1.00
R1832:Col16a1	UTSW	4	130077057	splice site	probably null
R1861:Col16a1	UTSW	4	130061724	unclassified	probably benign
R1862:Col16a1	UTSW	4	130092782	critical splice donor site	probably null
R1981:Col16a1	UTSW	4	130065443	missense	unknown
R2265:Col16a1	UTSW	4	130052918	missense	probably benign	0.02
R2269:Col16a1	UTSW	4	130052918	missense	probably benign	0.02
R2291:Col16a1	UTSW	4	130067040	missense	unknown
R3176:Col16a1	UTSW	4	130057999	missense	probably damaging	0.99
R3276:Col16a1	UTSW	4	130057999	missense	probably damaging	0.99
R3552:Col16a1	UTSW	4	130077041	missense	probably benign	0.10
R4049:Col16a1	UTSW	4	130068752	missense	probably damaging	1.00
R4241:Col16a1	UTSW	4	130099050	missense	probably damaging	0.98
R4327:Col16a1	UTSW	4	130094551	critical splice donor site	probably null
R4591:Col16a1	UTSW	4	130061799	splice site	probably null
R4664:Col16a1	UTSW	4	130062090	unclassified	probably benign
R4803:Col16a1	UTSW	4	130055108	unclassified	probably benign
R4925:Col16a1	UTSW	4	130054176	missense	probably damaging	1.00
R4961:Col16a1	UTSW	4	130054479	splice site	probably null
R5016:Col16a1	UTSW	4	130079195	missense	probably benign	0.31
R5027:Col16a1	UTSW	4	130079195	missense	probably benign	0.31
R5085:Col16a1	UTSW	4	130054171	missense	probably damaging	1.00
R5088:Col16a1	UTSW	4	130079195	missense	probably benign	0.31
R5089:Col16a1	UTSW	4	130079195	missense	probably benign	0.31
R5408:Col16a1	UTSW	4	130093105	utr 3 prime	probably benign
R5472:Col16a1	UTSW	4	130092771	utr 3 prime	probably benign
R5564:Col16a1	UTSW	4	130053358	missense	probably damaging	1.00
R5597:Col16a1	UTSW	4	130058304	missense	probably damaging	1.00
R5703:Col16a1	UTSW	4	130053299	missense	probably damaging	0.96
R6054:Col16a1	UTSW	4	130061722	unclassified	probably benign
R6226:Col16a1	UTSW	4	130055089	unclassified	probably benign
R6362:Col16a1	UTSW	4	130066190	missense	unknown
R6448:Col16a1	UTSW	4	130058988	missense	probably damaging	1.00
R6449:Col16a1	UTSW	4	130066693	missense	unknown
R6502:Col16a1	UTSW	4	130055994	missense	probably damaging	1.00
R6949:Col16a1	UTSW	4	130059323	missense	probably damaging	1.00
R6969:Col16a1	UTSW	4	130093087	utr 3 prime	probably benign
R7086:Col16a1	UTSW	4	130052980	splice site	probably null
R7375:Col16a1	UTSW	4	130065501	missense	unknown
R7703:Col16a1	UTSW	4	130096502	missense	unknown
R7808:Col16a1	UTSW	4	130073264	missense	unknown
R7904:Col16a1	UTSW	4	130054208	nonsense	probably null
R7936:Col16a1	UTSW	4	130096871	critical splice acceptor site	probably null
R7981:Col16a1	UTSW	4	130086554	critical splice donor site	probably null
R8161:Col16a1	UTSW	4	130060469	missense	unknown
R8178:Col16a1	UTSW	4	130053477	missense	unknown
R8266:Col16a1	UTSW	4	130065431	missense	unknown
R8312:Col16a1	UTSW	4	130054451	missense	unknown
Z1176:Col16a1	UTSW	4	130072878	missense	unknown

Predicted Primers

PCR Primer
(F):5'- TACACCAAGCCAAAGGGATG -3'
(R):5'- TCTCTAAAGACCCCAGGTGTG -3'

Sequencing Primer
(F):5'- GGGATGAAGAAATGACTTGCTTTC -3'
(R):5'- TGTGCTGTGCAAAGCCAAC -3'

Posted On

2019-12-04