The UMD-MSH2 mutations database
Intronic mutations

This function evaluates the potential pathogenic impact of intronic mutations.

Intronic mutations can interact with the splicing process either by disrupting a wild type donor or acceptor splice sits but also a branch point. In addition, it can result in the creation of a new (cryptic) site that can be used in place of the wt site. (Note that an intronic mutation can also interacts with regulatory sequences).
The consensus value (CV) of splice sites is calculated with the UMD algorithm. A value >70 is associated with a potentially functional site. When a mutation affects a site both the CV of the mutant sequence and the variation of the CV (in comparison to the wt) should be taken into account. Usually, a variation of 10% or more is associated with a splice recognition alteration (*).
A color code allows a rapid interpretation of CVs: Strong splice site; Medium splice site; weak splice site and not a splice site.

1228 records found

Mutation	Splice site type	Wild type sequence	CV	Mutant type sequence	CV	Variation (%)
c.IVS1+98T>C (c.211+98T>C)
c.IVS1+9C>G (c.211+9C>G)
c.IVS1+2T>C (c.211+2T>C)	Donor	CAGgtgagg	96.9 _	CAGgcgagg	70.1 _ *	-27.7 %
c.IVS1-4del (c.212-4del)	Acceptor	tttttttttaagGA	87.5 _	tttttttttaagGA	87.5 _	0 %
c.IVS2+1G>T (c.366+1G>T)	Donor	AAGgtaatt	86.7 _	AAGttaatt	59.9 _ *	-30.9 %
c.IVS2+1G>A (c.366+1G>A)	Donor	AAGgtaatt	86.7 _	AAGataatt	59.9 _ *	-30.9 %
c.IVS2-27A>C (c.367-27A>C)
c.IVS2-46delC (c.367-46delC)	Cryptic Donor?	aagagtttg	17.3 _	agagtttgt	69.8 _ *	75.2 %
c.IVS2-49A>T (c.367-49A>T)
c.IVS3+1G>T (c.645+1G>T)	Donor	CAGgtaagc	97.8 _	CAGttaagc	71 _ *	-27.4 %
c.IVS3+1G>C (c.645+1G>C)	Donor	CAGgtaagc	97.8 _	CAGctaagc	71 _ *	-27.4 %
c.IVS3+1G>A (c.645+1G>A)	Donor	CAGgtaagc	97.8 _	CAGataagc	71 _ *	-27.4 %
c.IVS3+35C>T (c.645+35C>T)
c.IVS3-1G>C (c.646-1G>C)	Acceptor	ctttcaaaatagAT	77.8 _	ctttcaaaatacAT	48.9 _ *	-37.2 %
c.IVS3-2A>G (c.646-2A>G)	Acceptor	ctttcaaaatagAT	77.8 _	ctttcaaaatggAT	48.9 _ *	-37.2 %
c.IVS3-1G>T (c.646-1G>T)	Acceptor	ctttcaaaatagAT	77.8 _	ctttcaaaatatAT	48.9 _ *	-37.2 %
c.IVS3-20A>C (c.646-20A>C)
c.IVS4+1del (c.792+1del)	Donor	CAGgtacat	79 _	CAGgtacat	79 _	0 %
c.IVS4+1G>C (c.792+1G>C)	Donor	CAGgtacat	79 _	CAGctacat	52.2 _ *	-34 %
c.IVS4+96A>T (c.792+96A>T)
c.IVS4-23G>A (c.793-23G>A)
c.IVS4-2A>C (c.793-2A>C)	Acceptor	tcttaattttagGT	84 _	tcttaattttcgGT	55 _ *	-34.5 %
c.IVS4-5T>C (c.793-5T>C)	Acceptor	tcttaattttagGT	84 _	tcttaatcttagGT	83.1 _	-1.1 %
c.IVS5+3A>T (c.942+3A>T)	Donor	CAGgtaaaa	99.2 _	CAGgttaaa	81.3 _ *	-18 %
c.IVS4-1G>A (c.793-1G>A)	Acceptor	tcttaattttagGT	84 _	tcttaattttaaGT	55 _ *	-34.5 %
c.IVS5+124T>A (c.942+124T>A)
c.IVS5+2T>A (c.942+2T>A)	Donor	CAGgtaaaa	85.5 _	CAGgaaaaa	58.7 _ *	-31.4 %
c.IVS5+2T>G (c.942+2T>G)	Donor	CAGgtaaaa	85.5 _	CAGggaaaa	58.7 _ *	-31.4 %
c.IVS5+28del2 (c.942+28del2)	Cryptic Donor?	aaagggtta	37 _	agggttaaa	74.7 _ *	50.4 %
c.IVS5+1del2 (c.942+1del2)	Donor	CAGgtaaaa	85.5 _	CAGaaaata	31.7 _ *	-63 %
c.IVS5+19del11 (c.942+19del11)	Cryptic Donor?	aaaaaaaaa	20.3 _	agggttaaa	74.7 _ *	72.8 %
c.IVS5+3A>C (c.942+3A>C)	Donor	CAGgtaaaa	99.2 _	CAGgtcaaa	81.1 _ *	-18.2 %
c.IVS5-2A>C (c.943-2A>C)	Acceptor	tttgtttactagGG	83.4 _	tttgtttactcgGG	54.4 _ *	-34.7 %
c.IVS6-10T>C (c.1077-10T>C)	Acceptor	aatttatttcagAT	85.1 _	aacttatttcagAT	84.4 _	-0.8 %
c.IVS6-80G>A (c.1077-80G>A)
c.IVS6+1G>A (c.1076+1G>A)	Donor	GAGgtatgt	89.4 _	GAGatatgt	62.6 _ *	-30 %
c.IVS6-2A>C (c.1077-2A>C)	Acceptor	aatttatttcagAT	85.1 _	aatttatttccgAT	56.2 _ *	-34 %
c.IVS6-1G>T (c.1077-1G>T)	Acceptor	aatttatttcagAT	85.1 _	aatttatttcatAT	56.2 _ *	-34 %
c.IVS6-58G>T (c.1077-58G>T)
c.IVS6-43T>G (c.1077-43T>G)
c.IVS6-11delATTTA (c.1077-11delATTTA)	Acceptor	aatttatttcagAT	85.1 _	atttcagATTTGAA	45.8 _ *	-46.1 %
c.IVS6+2T>A (c.1076+2T>A)	Donor	GAGgtatgt	89.4 _	GAGgaatgt	62.6 _ *	-30 %
c.IVS6+5G>T (c.1076+5G>T)	Donor	GAGgtatgt	89.4 _	GAGgtattt	77.1 _ *	-13.8 %
c.IVS6-10T>A (c.1077-10T>A)	Acceptor	aatttatttcagAT	85.1 _	aaattatttcagAT	81.9 _	-3.8 %
c.IVS7+3A>C (c.1276+3A>C)	Donor	AAGgtaaca	97.3 _	AAGgtcaca	83.2 _ *	-14.6 %
c.IVS7+51C>A (c.1276+51C>A)
c.IVS7-67A>G (c.1277-67A>G)	Cryptic Acceptor?	tatctcagtcaaaat	53.7 _	tatctcagtcaGaat	82.7 _ *	35 %
c.IVS7+2T>A (c.1276+2T>A)	Donor	AAGgtaaca	84.7 _	AAGgaaaca	57.9 _ *	-31.7 %
c.IVS7-1G>A (c.1277-1G>A)	Acceptor	actttcttttagGA	84.4 _	actttcttttaaGA	55.5 _ *	-34.3 %
c.IVS7-11delCTT (c.1277-11delCTT)	Acceptor	actttcttttagGA	84.4 _	atcttttagGAAAA	46.9 _ *	-44.4 %
c.IVS7+11A>G (c.1276+11A>G)	Cryptic Donor?	gtgattttg	38.6 _	gtggttttg	65.4 _ *	41 %
c.IVS7-2A>C (c.1277-2A>C)	Acceptor	actttcttttagGA	84.4 _	actttcttttcgGA	55.5 _ *	-34.3 %
c.IVS7-2A>G (c.1277-2A>G)	Acceptor	actttcttttagGA	84.4 _	actttcttttggGA	55.5 _ *	-34.3 %
c.IVS7-7delCTTT (c.1277-7delCTTT)	Acceptor	actttcttttagGA	84.4 _	acttttagGAAAAA	43.9 _ *	-48 %
c.IVS7-8T>C (c.1277-8T>C)	Acceptor	actttcttttagGA	84.4 _	acttccttttagGA	85 _	0.7 %
c.IVS7-10T>C (c.1277-10T>C)	Acceptor	actttcttttagGA	84.4 _	accttcttttagGA	83.7 _	-0.8 %
c.IVS7+47T>A (c.1276+47T>A)
c.IVS7+1G>A (c.1276+1G>A)	Donor	AAGgtaaca	84.7 _	AAGataaca	57.9 _ *	-31.7 %
c.IVS8+104C>T (c.1386+104C>T)
c.IVS8+1G>T (c.1386+1G>T)	Donor	CAGgtatgc	89 _	CAGttatgc	62.2 _ *	-30.1 %
c.IVS8+28A>G (c.1386+28A>G)	Cryptic Donor?	gcagtagtt	62.3 _	gcGgtagtt	72.8 _ *	14.5 %
c.IVS8+1G>A (c.1386+1G>A)	Donor	CAGgtatgc	89 _	CAGatatgc	62.2 _ *	-30.1 %
c.IVS8+52G>C (c.1386+52G>C)
c.IVS8-77T>G (c.1387-77T>G)
c.IVS8-8G>T (c.1387-8G>T)	Acceptor	ttctgtttgcagGT	95.1 _	ttctttttgcagGT	97 _	2 %
c.IVS8-5del (c.1387-5del)	Acceptor	ttctgtttgcagGT	95.1 _	ttctgtttgcagGT	95.1 _	0 %
c.IVS8-72G>A (c.1387-72G>A)	Cryptic Acceptor?	ttaagtgggaggaaa	40.7 _	ttaagtgggaAgaaa	69.6 _ *	41.6 %
c.IVS9+111T>C (c.1510+111T>C)
c.IVS9+115A>G (c.1510+115A>G)
c.IVS9+118T>C (c.1510+118T>C)
c.IVS9-91G>T (c.1511-91G>T)
c.IVS9-9A>T (c.1511-9A>T)	Acceptor	ttgattatcaagGC	79 _	ttgtttatcaagGC	82.2 _	3.9 %
c.IVS9-1G>A (c.1511-1G>A)	Acceptor	ttgattatcaagGC	79 _	ttgattatcaaaGC	50.1 _ *	-36.6 %
c.IVS9-41G>C (c.1511-41G>C)
c.IVS9+29delAAT (c.1510+29delAAT)
c.IVS9-29T>C (c.1511-29T>C)
c.IVS9+1G>C (c.1510+1G>C)	Donor	TTGgtaaga	90.9 _	TTGctaaga	64.1 _ *	-29.5 %
c.IVS10+12G>A (c.1661+12G>A)	Cryptic Donor?	caagtcgtt	63.7 _	caagtcatt	72.1 _ *	11.6 %
c.IVS10-9G>A (c.1662-9G>A)	Acceptor	ttcgatttgcagCA	87 _	ttcaatttgcagCA	86.8 _	-0.1 %
c.IVS10+1G>A (c.1661+1G>A)	Donor	CAGgtttgc	84 _	CAGatttgc	57.2 _ *	-31.9 %
c.IVS10+1G>T (c.1661+1G>T)	Donor	CAGgtttgc	84 _	CAGttttgc	57.2 _ *	-31.9 %
c.IVS10-18T>C (c.1662-18T>C)
c.IVS10-43C>T (c.1662-43C>T)	Alternative Branch Point?	tacacat	70.7 _	taTacat	46.9 _ *	-33.6 %
c.IVS10-2A>G (c.1662-2A>G)	Acceptor	ttcgatttgcagCA	87 _	ttcgatttgcggCA	58 _ *	-33.3 %
c.IVS11+107A>G (c.1759+107A>G)
c.IVS11+183G>A (c.1759+183G>A)
c.IVS11-62G>A (c.1760-62G>A)	Cryptic Acceptor?	gtatttttacggctt	58.3 _	gtatttttacAgctt	87.2 _ *	33.2 %
c.IVS11+2T>G (c.1759+2T>G)	Donor	CAGgtaaac	85.7 _	CAGggaaac	58.8 _ *	-31.3 %
c.IVS11+9A>C (c.1759+9A>C)
c.IVS11-44A>C (c.1760-44A>C)
c.IVS11+1G>T (c.1759+1G>T)	Donor	CAGgtaaac	85.7 _	CAGttaaac	58.8 _ *	-31.3 %
c.IVS11-55A>G (c.1760-55A>G)	Cryptic Donor?	tatatctgt	46.5 _	tatgtctgt	73.3 _ *	36.6 %
c.IVS12+1G>A (c.2005+1G>A)	Donor	CTGgtaaaa	80.7 _	CTGataaaa	53.9 _ *	-33.2 %
c.IVS12-42delAGAA (c.2006-42delAGAA)	Cryptic Acceptor?	tagtagcagaaagaa	44.5 _	tagtagcagaagttt	69.9 _ *	36.4 %
c.IVS12-6T>C (c.2006-6T>C)	Acceptor	tttgttttgtagGC	86.1 _	tttgttctgtagGC	86.7 _	0.8 %
c.IVS12+2del (c.2005+2del)	Donor	CTGgtaaaa	80.7 _	CTGgtaaaa	80.7 _	0 %
c.IVS12+9C>A (c.2005+9C>A)
c.IVS12+3A>T (c.2005+3A>T)	Donor	CTGgtaaaa	84 _	CTGgttaaa	66.1 _ *	-21.3 %
c.IVS12-2A>G (c.2006-2A>G)	Acceptor	tttgttttgtagGC	86.1 _	tttgttttgtggGC	57.1 _ *	-33.6 %
c.IVS12-50delTAG (c.2006-50delTAG)	Cryptic Acceptor?	attagtagcagaaag	12.2 _	attagcagaaagaag	70 _ *	82.5 %
c.IVS12-5T>C (c.2006-5T>C)	Acceptor	tttgttttgtagGC	86.1 _	tttgtttcgtagGC	85.2 _	-1 %
c.IVS13-10T>G (c.2211-10T>G)	Cryptic Acceptor?	tcatgtaattatgtg	47.7 _	tcatgtaattaGgtg	76.7 _ *	37.7 %
c.IVS13-51A>G (c.2211-51A>G)	Cryptic Donor?	tatgtgtat	65 _	tatgtgtgt	77.2 _ *	15.8 %
c.IVS13-6C>A (c.2211-6C>A)	Cryptic Donor?	tatgtgctt	64.9 _	tatgtgatt	73.7 _ *	11.9 %
c.IVS13-1G>A (c.2211-1G>A)	Acceptor	tatgtgcttcagGT	89.1 _	tatgtgcttcaaGT	60.1 _ *	-32.5 %
c.IVS13-15A>C (c.2211-15A>C)
c.IVS13+7G>T (c.2210+7G>T)
c.IVS13-14A>C (c.2211-14A>C)	Acceptor	tatgtgcttcagGT	89.1 _	ctatgtgcttcagGT	21.4 _ *	-76 %
c.IVS14-38T>G (c.2459-38T>G)	Alternative Branch Point?	ttctcat	94.6 _	ttcGcat	75.7 _ *	-20 %
c.IVS14-8T>G (c.2459-8T>G)	Acceptor	aatttcttatagGT	83.2 _	aattgcttatagGT	81.3 _	-2.3 %
c.IVS14-1G>T (c.2459-1G>T)	Acceptor	aatttcttatagGT	83.2 _	aatttcttatatGT	54.3 _ *	-34.8 %
c.IVS14-3T>G (c.2459-3T>G)	Cryptic Acceptor?	caaatttcttatagG	44.8 _	caaatttcttaGagG	73.8 _ *	39.2 %
c.IVS14+10A>C (c.2458+10A>C)
c.IVS14+36G>A (c.2458+36G>A)	Cryptic Acceptor?	ttcagaacttggtaa	44.3 _	ttcagaacttAgtaa	73.2 _ *	39.5 %
c.IVS14+8C>T (c.2458+8C>T)
c.IVS14-12A>G (c.2459-12A>G)	Cryptic Acceptor?	acgcttccccaaatt	56.5 _	acgcttccccaGatt	85.5 _ *	33.9 %
c.IVS15+5G>T (c.2634+5G>T)	Donor	GAGgtttgt	84.4 _	GAGgttttt	72.1 _ *	-14.6 %
c.IVS15+1G>A (c.2634+1G>A)	Donor	GAGgtttgt	84.4 _	GAGatttgt	57.6 _ *	-31.8 %
c.IVS15+1G>T (c.2634+1G>T)	Donor	GAGgtttgt	84.4 _	GAGttttgt	57.6 _ *	-31.8 %
c.IVS15+5G>C (c.2634+5G>C)	Donor	GAGgtttgt	84.4 _	GAGgtttct	72.4 _ *	-14.2 %
c.IVS15-8T>G (c.2635-8T>G)	Acceptor	catgtgtttcagCA	82.3 _	catgggtttcagCA	80.3 _	-2.3 %
c.IVS15-3C>T (c.2635-3C>T)	Acceptor	catgtgtttcagCA	82.3 _	catgtgttttagCA	74.6 _	-9.3 %
c.IVS15-3C>A (c.2635-3C>A)	Acceptor	catgtgtttcagCA	82.3 _	catgtgtttaagCA	72.9 _ *	-11.4 %
c.IVS15-112del (c.2635-112del)
c.IVS15-1G>T (c.2635-1G>T)	Acceptor	catgtgtttcagCA	82.3 _	catgtgtttcatCA	53.3 _ *	-35.2 %
c.IVS15-11A>G (c.2635-11A>G)	Cryptic Donor?	cacatgtgt	52.2 _	cacgtgtgt	79 _ *	34 %
c.IVS15-1G>C (c.2635-1G>C)	Acceptor	catgtgtttcagCA	82.3 _	catgtgtttcacCA	53.3 _ *	-35.2 %
c.IVS15-24A>G (c.2635-24A>G)	Cryptic Acceptor?	tttaattactaatgg	48 _	tttaattactaGtgg	77 _ *	37.6 %
c.IVS15-106T>A (c.2635-106T>A)
c.IVS15-26T>C (c.2635-26T>C)	Alternative Branch Point?	tactaat	81.8 _	tacCaat	65.2 _ *	-20.2 %