The UMD-DMD France 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.

221 records found

Mutation	Splice site type	Wild type sequence	CV	Mutant type sequence	CV	Variation (%)
c.IVS1+16C>G (c.31+16C>G)	Cryptic Acceptor?	GTACAAAGTAACTAA	36.2 _	GTACAAAGTAAGTAA	65.1 _ *	44.4 %
c.IVS1+1G>T (c.31+1G>T)	Donor	GTTgtaagt	82.6 _	GTTttaagt	55.8 _ *	-32.5 %
c.IVS1+5G>C (c.31+5G>C)	Donor	GTTgtaagt	82.6 _	GTTgtaact	70.6 _ *	-14.5 %
c.IVS2+1G>A (c.93+1G>A)	Donor	AAGgtaaga	96.7 _	AAGataaga	69.9 _ *	-27.7 %
c.IVS3+1G>A (c.186+1G>A)	Donor	CTGgtatgt	86.4 _	CTGatatgt	59.6 _ *	-31 %
c.IVS4-463A>G (c.265-463A>G)	Cryptic Donor?	GAGataaga	69.1 _	GAGgtaaga	95.9 _ *	28 %
c.IVS5+1G>A (c.357+1G>A)	Donor	CAGgtaaga	97.7 _	CAGataaga	70.8 _ *	-27.5 %
c.IVS5+1G>C (c.357+1G>C)	Donor	CAGgtaaga	97.7 _	CAGctaaga	70.8 _ *	-27.5 %
c.IVS5-1G>T (c.358-1G>T)	Acceptor	ttccacatgtagGT	83.8 _	ttccacatgtatGT	54.8 _ *	-34.6 %
c.IVS5-1G>A (c.358-1G>A)	Acceptor	ttccacatgtagGT	83.8 _	ttccacatgtaaGT	54.8 _ *	-34.6 %
c.IVS5-2A>G (c.358-2A>G)	Acceptor	ttccacatgtagGT	83.8 _	ttccacatgtggGT	54.8 _ *	-34.6 %
c.IVS6-16T>A (c.531-16T>A)	Cryptic Acceptor?	TATGTGTGTATGTGT	41.6 _	TATGTGTGTAAGTGT	70.5 _ *	41 %
c.IVS6-2A>C (c.531-2A>C)	Acceptor	tatgtgttttagGC	79.9 _	tatgtgttttcgGC	51 _ *	-36.2 %
c.IVS6+2T>G (c.530+2T>G)	Donor	TAGgtaaga	95.7 _	TAGggaaga	68.8 _ *	-28 %
c.IVS6+2T>C (c.530+2T>C)	Donor	TAGgtaaga	95.7 _	TAGgcaaga	68.8 _ *	-28 %
c.IVS6-1G>T (c.531-1G>T)	Acceptor	tatgtgttttagGC	79.9 _	tatgtgttttatGC	51 _ *	-36.2 %
c.IVS7+1G>T (c.649+1G>T)	Donor	AAGgttggt	85.7 _	AAGtttggt	58.8 _ *	-31.3 %
c.IVS7+5G>A (c.649+5G>A)	Donor	AAGgttggt	85.7 _	AAGgttgat	73.5 _ *	-14.2 %
c.IVS7+2T>C (c.649+2T>C)	Donor	AAGgttggt	85.7 _	AAGgctggt	58.8 _ *	-31.3 %
c.IVS8+2T>C (c.831+2T>C)	Donor	CAGgtaaag	85.9 _	CAGgcaaag	59.1 _ *	-31.2 %
c.IVS8-15A>G (c.832-15A>G)	Cryptic Acceptor?	CCACTCCCCCAAACC	58.1 _	CCACTCCCCCAGACC	87 _ *	33.3 %
c.IVS9-1G>A (c.961-1G>A)	Acceptor	tttattgtgcagCA	86.7 _	tttattgtgcaaCA	57.8 _ *	-33.4 %
c.IVS10+1G>T (c.1149+1G>T)	Donor	GAGgtaaac	83.9 _	GAGttaaac	57.1 _ *	-32 %
c.IVS10-2A>G (c.1150-2A>G)	Acceptor	cttctttgtcagGG	91 _	cttctttgtcggGG	62 _ *	-31.8 %
c.IVS11+1G>T (c.1331+1G>T)	Donor	CAAgtaagt	89.4 _	CAAttaagt	62.6 _ *	-30 %
c.IVS11-9A>G (c.1332-9A>G)	Cryptic Acceptor?	GGCTTCTTTCAAATT	58.5 _	GGCTTCTTTCAGATT	87.4 _ *	33.1 %
c.IVS12+1G>T (c.1482+1G>T)	Donor	AAGgtaggt	90.7 _	AAGttaggt	63.9 _ *	-29.6 %
c.IVS13-1G>A (c.1603-1G>A)	Acceptor	tctcttctccagGT	95.9 _	tctcttctccaaGT	67 _ *	-30.2 %
c.IVS15+601A>G (c.1812+601A>G)	Cryptic Donor?	GAGataaga	69.1 _	GAGgtaaga	95.9 _ *	28 %
c.IVS16+1G>T (c.1992+1G>T)	Donor	CAGgttagt	95 _	CAGtttagt	68.1 _ *	-28.3 %
c.IVS16-3C>G (c.1993-3C>G)	Acceptor	tacttctcacagAT	89.5 _	tacttctcagagAT	79.2 _ *	-11.5 %
c.IVS17-2A>G (c.2169-2A>G)	Acceptor	ttgctgtcttagGT	82.6 _	ttgctgtcttggGT	53.7 _ *	-35 %
c.IVS17-1G>A (c.2169-1G>A)	Acceptor	ttgctgtcttagGT	82.6 _	ttgctgtcttaaGT	53.7 _ *	-35 %
c.IVS17-2A>T (c.2169-2A>T)	Acceptor	ttgctgtcttagGT	82.6 _	ttgctgtctttgGT	53.7 _ *	-35 %
c.IVS18+1G>T (c.2292+1G>T)	Donor	AATgtaggt	79.8 _	AATttaggt	53 _ *	-33.6 %
c.IVS18+2T>C (c.2292+2T>C)	Donor	AATgtaggt	79.8 _	AATgcaggt	53 _ *	-33.6 %
c.IVS18+1G>A (c.2292+1G>A)	Donor	AATgtaggt	79.8 _	AATataggt	53 _ *	-33.6 %
c.IVS18-5del7 (c.2293-5del7)	Acceptor	ctcatgctgcagGC	90.1 _	ctcatgcATAGAGCG	19.2 _ *	-78.6 %
c.IVS18-1G>T (c.2293-1G>T)	Acceptor	ctcatgctgcagGC	90.1 _	ctcatgctgcatGC	61.2 _ *	-32.1 %
c.IVS18-1G>A (c.2293-1G>A)	Acceptor	ctcatgctgcagGC	90.1 _	ctcatgctgcaaGC	61.2 _ *	-32.1 %
c.IVS19+2T>C (c.2380+2T>C)	Donor	ATGgtaatt	82 _	ATGgcaatt	55.1 _ *	-32.7 %
c.IVS19-2A>G (c.2381-2A>G)	Acceptor	ttttctttctagAG	87.5 _	ttttctttctggAG	58.6 _ *	-33.1 %
c.IVS20+2T>G (c.2622+2T>G)	Donor	AAGgtaaga	96.7 _	AAGggaaga	69.9 _ *	-27.7 %
c.IVS20+1G>A (c.2622+1G>A)	Donor	AAGgtaaga	96.7 _	AAGataaga	69.9 _ *	-27.7 %
c.IVS20-3C>G (c.2623-3C>G)	Acceptor	tctatggcacagGA	86 _	tctatggcagagGA	75.7 _ *	-12 %
c.IVS21-1G>T (c.2804-1G>T)	Acceptor	cttttgataaagTT	77.9 _	cttttgataaatTT	48.9 _ *	-37.2 %
c.IVS21-2A>C (c.2804-2A>C)	Acceptor	cttttgataaagTT	77.9 _	cttttgataacgTT	48.9 _ *	-37.2 %
c.IVS21-2A>G (c.2804-2A>G)	Acceptor	cttttgataaagTT	77.9 _	cttttgataaggTT	48.9 _ *	-37.2 %
c.IVS21-2A>T (c.2804-2A>T)	Acceptor	cttttgataaagTT	77.9 _	cttttgataatgTT	48.9 _ *	-37.2 %
c.IVS21+1delG (c.2803+1delG)	Donor	CAAgtaagt	89.4 _	CAAtaagtt	15.1 _ *	-83.1 %
c.IVS22+1G>T (c.2949+1G>T)	Donor	CAGgtctgt	86.2 _	CAGttctgt	59.3 _ *	-31.1 %
c.IVS24+1G>A (c.3276+1G>A)	Donor	AGAgtaaga	81.3 _	AGAataaga	54.4 _ *	-33 %
c.IVS24-1G>T (c.3277-1G>T)	Acceptor	ttattttcttagCT	81.7 _	ttattttcttatCT	52.8 _ *	-35.4 %
c.IVS25+2240A>G (c.3432+2240A>G)	Cryptic Acceptor?	CTACAGACAAAATAA	40.9 _	CTACAGACAAAGTAA	69.8 _ *	41.5 %
c.IVS26+2T>A (c.3603+2T>A)	Donor	AAGgtaaaa	84.5 _	AAGgaaaaa	57.7 _ *	-31.7 %
c.IVS26+1G>T (c.3603+1G>T)	Donor	AAGgtaaaa	84.5 _	AAGttaaaa	57.7 _ *	-31.7 %
c.IVS26+1G>A (c.3603+1G>A)	Donor	AAGgtaaaa	84.5 _	AAGataaaa	57.7 _ *	-31.7 %
c.IVS27+1G>A (c.3786+1G>A)	Donor	GAAgtcagt	82.6 _	GAAatcagt	55.8 _ *	-32.5 %
c.IVS32+1G>A (c.4518+1G>A)	Donor	GTGgtatgt	84.7 _	GTGatatgt	57.9 _ *	-31.7 %
c.IVS32+1G>T (c.4518+1G>T)	Donor	GTGgtatgt	84.7 _	GTGttatgt	57.9 _ *	-31.7 %
c.IVS32+2T>C (c.4518+2T>C)	Donor	GTGgtatgt	84.7 _	GTGgcatgt	57.9 _ *	-31.7 %
c.IVS32+2T>G (c.4518+2T>G)	Donor	GTGgtatgt	84.7 _	GTGggatgt	57.9 _ *	-31.7 %
c.IVS32+5G>A (c.4518+5G>A)	Donor	GTGgtatgt	84.7 _	GTGgtatat	72.5 _ *	-14.4 %
c.IVS32+6T>A (c.4518+6T>A)	Donor	GTGgtatgt	84.7 _	GTGgtatga	82.4 _	-2.8 %
c.IVS34+2T>C (c.4845+2T>C)	Donor	AAGgtaaaa	84.5 _	AAGgcaaaa	57.7 _ *	-31.7 %
c.IVS34-1469A>G (c.4846-1469A>G)	Cryptic Donor?	TATattata	40.6 _	TATgttata	67.5 _ *	39.8 %
c.IVS35-2A>G (c.5026-2A>G)	Acceptor	tgtacaattaagGA	76.3 _	tgtacaattaggGA	47.4 _ *	-37.9 %
c.IVS36-3T>G (c.5155-3T>G)	Cryptic Acceptor?	CTCATGGAATATAGC	43.6 _	CTCATGGAATAGAGC	72.6 _ *	39.9 %
c.IVS38-3C>G (c.5449-3C>G)	Acceptor	gtttttgatcagAA	84.2 _	gtttttgatgagAA	73.9 _ *	-12.2 %
c.IVS40+18T>A (c.5739+18T>A)	Cryptic Acceptor?	TGTTTTAGAATGTCA	44.2 _	TGTTTTAGAAAGTCA	73.2 _ *	39.6 %
c.IVS40+362A>G (c.5739+362A>G)	Cryptic Donor?	CACatcagt	57.1 _	CACgtcagt	84 _ *	32 %
c.IVS42-1G>A (c.6118-1G>A)	Acceptor	tttatattacagAA	88.5 _	tttatattacaaAA	59.5 _ *	-32.7 %
c.IVS43+1G>T (c.6290+1G>T)	Donor	AGGgtaggt	85.8 _	AGGttaggt	59 _ *	-31.3 %
c.IVS43-1G>A (c.6291-1G>A)	Acceptor	ttttacctgcagGC	95.9 _	ttttacctgcaaGC	67 _ *	-30.2 %
c.IVS43+2T>C (c.6290+2T>C)	Donor	AGGgtaggt	85.8 _	AGGgcaggt	59 _ *	-31.3 %
c.IVS43+5G>C (c.6290+5G>C)	Donor	AGGgtaggt	85.8 _	AGGgtagct	73.8 _ *	-14 %
c.IVS44+1G>A (c.6438+1G>A)	Donor	AAGgtaagt	99 _	AAGataagt	72.2 _ *	-27.1 %
c.IVS44+1delG (c.6438+1delG)	Donor	AAGgtaagt	99 _	AAGtaagtt	24.7 _ *	-75 %
c.IVS44+2insTT (c.6438+2insTT)	Donor	AAGgtaagt	99 _	AAGgtttaa	70.7 _ *	-28.6 %
c.IVS45-1G>C (c.6615-1G>C)	Acceptor	ttctttctccagGC	97.4 _	ttctttctccacGC	68.5 _ *	-29.7 %
c.IVS45+2T>C (c.6614+2T>C)	Donor	GAGgtaggg	88 _	GAGgcaggg	61.1 _ *	-30.5 %
c.IVS45-2A>T (c.6615-2A>T)	Acceptor	ttctttctccagGC	97.4 _	ttctttctcctgGC	68.5 _ *	-29.7 %
c.IVS45+1G>T (c.6614+1G>T)	Donor	GAGgtaggg	88 _	GAGttaggg	61.1 _ *	-30.5 %
c.IVS45+1G>A (c.6614+1G>A)	Donor	GAGgtaggg	88 _	GAGataggg	61.1 _ *	-30.5 %
c.IVS46+2T>C (c.6762+2T>C)	Donor	AAGgtaatt	86.7 _	AAGgcaatt	59.9 _ *	-30.9 %
c.IVS47-2A>G (c.6913-2A>G)	Acceptor	ttttcctttcagGT	98.7 _	ttttcctttcggGT	69.7 _ *	-29.3 %
c.IVS47-4037T>G (c.6913-4037T>G)	Cryptic Acceptor?	TAATCCCCACATGTC	62.5 _	TAATCCCCACAGGTC	91.4 _ *	31.7 %
c.IVS48+1G>T (c.7098+1G>T)	Donor	CAGgtaggg	89.7 _	CAGttaggg	62.9 _ *	-29.9 %
c.IVS49-3A>G (c.7201-3A>G)	Cryptic Acceptor?	CTTTTCTGTTAAAGA	52.8 _	CTTTTCTGTTAGAGA	81.8 _ *	35.4 %
c.IVS50-2A>G (c.7310-2A>G)	Acceptor	aaaatattttagCT	70 _	aaaatattttggCT	41 _ *	-41.4 %
c.IVS50+2T>A (c.7309+2T>A)	Donor	CCTgtaagt	84.4 _	CCTgaaagt	57.5 _ *	-31.8 %
c.IVS50-1G>A (c.7310-1G>A)	Acceptor	aaaatattttagCT	70 _	aaaatattttaaCT	41 _ *	-41.4 %
c.IVS50+1G>A (c.7309+1G>A)	Donor	CCTgtaagt	84.4 _	CCTataagt	57.5 _ *	-31.8 %
c.IVS54+11C>T (c.8027+11C>T)
c.IVS54+1G>T (c.8027+1G>T)	Donor	AAGgtatga	87.9 _	AAGttatga	61.1 _ *	-30.5 %
c.IVS54+1G>A (c.8027+1G>A)	Donor	AAGgtatga	87.9 _	AAGatatga	61.1 _ *	-30.5 %
c.IVS55+5G>A (c.8217+5G>A)	Donor	CAAgtaagt	89.4 _	CAAgtaaat	77.3 _ *	-13.6 %
c.IVS55+23A>G (c.8217+23A>G)
c.IVS55-2A>G (c.8218-2A>G)	Acceptor	gctgtcctgtagGA	82.2 _	gctgtcctgtggGA	53.3 _ *	-35.2 %
c.IVS55-1G>C (c.8218-1G>C)	Acceptor	gctgtcctgtagGA	82.2 _	gctgtcctgtacGA	53.3 _ *	-35.2 %
c.IVS56-1G>A (c.8391-1G>A)	Acceptor	gttctttttcagGT	93.3 _	gttctttttcaaGT	64.4 _ *	-31 %
c.IVS56+1G>A (c.8390+1G>A)	Donor	TAGgtagga	87.3 _	TAGatagga	60.5 _ *	-30.7 %
c.IVS56+1delG (c.8390+1delG)	Donor	TAGgtagga	87.3 _	TAGtaggat	22.7 _ *	-74 %
c.IVS58-2A>G (c.8669-2A>G)	Acceptor	ttgccaatttagAG	77.7 _	ttgccaatttggAG	48.7 _ *	-37.3 %
c.IVS58+1G>C (c.8668+1G>C)	Donor	GAGgtaatt	85.9 _	GAGctaatt	59.1 _ *	-31.2 %
c.IVS58+1delG (c.8668+1delG)	Donor	GAGgtaatt	85.9 _	GAGtaattt	23.4 _ *	-72.7 %
c.IVS60-15519G>T (c.9085-15519G>T)	Cryptic Donor?	AAGggaagc	70 _	AAGgtaagc	96.9 _ *	27.7 %
c.IVS60-1G>A (c.9085-1G>A)	Acceptor	ttttcctcccagGT	98.5 _	ttttcctcccaaGT	69.5 _ *	-29.4 %
c.IVS61+1G>A (c.9163+1G>A)	Donor	CCAgtaagt	84.7 _	CCAataagt	57.8 _ *	-31.7 %
c.IVS61+2T>G (c.9163+2T>G)	Donor	CCAgtaagt	84.7 _	CCAggaagt	57.8 _ *	-31.7 %
c.IVS61-2A>G (c.9164-2A>G)	Acceptor	ccttcttttcagCG	90.4 _	ccttcttttcggCG	61.5 _ *	-32 %
c.IVS62-647A>G (c.9225-647A>G)	Cryptic Acceptor?	ATTCAGGCCCAAGTA	56.9 _	ATTCAGGCCCAGGTA	85.9 _ *	33.7 %
c.IVS62+5G>C (c.9224+5G>C)	Donor	CAAgtaagt	89.4 _	CAAgtaact	77.4 _ *	-13.4 %
c.IVS62-2A>C (c.9225-2A>C)	Acceptor	tttgtgttttagCC	79.7 _	tttgtgttttcgCC	50.7 _ *	-36.3 %
c.IVS62-287C>A (c.9225-287C>A)
c.IVS62-1G>A (c.9225-1G>A)	Acceptor	tttgtgttttagCC	79.7 _	tttgtgttttaaCC	50.7 _ *	-36.3 %
c.IVS62+1G>A (c.9224+1G>A)	Donor	CAAgtaagt	89.4 _	CAAataagt	62.6 _ *	-30 %
c.IVS62-10T>A (c.9225-10T>A)	Cryptic Acceptor?	CTTTATGTTTTGTGT	50.1 _	CTTTATGTTTAGTGT	79 _ *	36.6 %
c.IVS63+2T>A (c.9286+2T>A)	Donor	TAGgtaagg	96.1 _	TAGgaaagg	69.3 _ *	-27.9 %
c.IVS64+1G>A (c.9361+1G>A)	Donor	GCTgtaagt	82.6 _	GCTataagt	55.8 _ *	-32.5 %
c.IVS65+1G>A (c.9563+1G>A)	Donor	TACgtacgt	78.2 _	TACatacgt	51.4 _ *	-34.3 %
c.IVS65+1215A>G (c.9563+1215A>G)	Cryptic Donor?	AAGataaga	69.9 _	AAGgtaaga	96.7 _ *	27.7 %
c.IVS65-427T>G (c.9564-427T>G)	Cryptic Acceptor?	GTTGCTGGTAATTTT	42.9 _	GTTGCTGGTAAGTTT	71.9 _ *	40.3 %
c.IVS65-2A>T (c.9564-2A>T)	Acceptor	tcttcataatagGG	82.5 _	tcttcataattgGG	53.6 _ *	-35.1 %
c.IVS65-2A>G (c.9564-2A>G)	Acceptor	tcttcataatagGG	82.5 _	tcttcataatggGG	53.6 _ *	-35.1 %
c.IVS66+6T>C (c.9649+6T>C)	Donor	GATgtaagt	87.4 _	GATgtaagc	85.2 _	-2.5 %
c.IVS66+1G>A (c.9649+1G>A)	Donor	GATgtaagt	87.4 _	GATataagt	60.5 _ *	-30.7 %
c.IVS67+6T>G (c.9807+6T>G)	Cryptic Donor?	AAGttattc	48.9 _	AAGgtattc	75.8 _ *	35.4 %
c.IVS67+5G>A (c.9807+5G>A)	Donor	TTTgtaagt	82.4 _	TTTgtaaat	70.2 _ *	-14.8 %
c.IVS67+4delA (c.9807+4delA)	Donor	TTTgtaagt	82.4 _	TTTgtagtg	59.8 _ *	-27.4 %
c.IVS68-2A>G (c.9975-2A>G)	Acceptor	gctctttatcagGT	87.9 _	gctctttatcggGT	59 _ *	-32.9 %
c.IVS68+1G>T (c.9974+1G>T)	Donor	CAGgtatta	76.5 _	CAGttatta	49.7 _ *	-35.1 %
c.IVS68+1G>C (c.9974+1G>C)	Donor	CAGgtatta	76.5 _	CAGctatta	49.7 _ *	-35.1 %
c.IVS69+1G>T (c.10086+1G>T)	Donor	CCGgtaagt	95.2 _	CCGttaagt	68.4 _ *	-28.2 %
c.IVS69+1G>A (c.10086+1G>A)	Donor	CCGgtaagt	95.2 _	CCGataagt	68.4 _ *	-28.2 %
c.IVS69+5G>C (c.10086+5G>C)	Donor	CCGgtaagt	95.2 _	CCGgtaact	83.2 _ *	-12.6 %
c.IVS69-2A>T (c.10087-2A>T)	Acceptor	tctcccttttagAC	84 _	tctccctttttgAC	55.1 _ *	-34.5 %
c.IVS70+1G>A (c.10223+1G>A)	Donor	AACgtgagt	86.9 _	AACatgagt	60 _ *	-30.9 %
c.IVS70-1InsT (c.10224-1InsT)	Acceptor	tttgttttgcagTC	89,5 _	tttgttttgcaTg	---	---
c.IVS70+2InsT (c.10223+2InsT)	Donor	AACgtgagt	86.9 _	AACgttgag	60.6 _ *	-30.3 %
c.IVS70+1G>T (c.10223+1G>T)	Donor	AACgtgagt	86.9 _	AACttgagt	60 _ *	-30.9 %
c.IVS70+3G>C (c.10223+3G>C)	Donor	AACgtgagt	84.1 _	AACgtcagt	77.2 _	-8.1 %
c.IVS70+5G>A (c.10223+5G>A)	Donor	AACgtgagt	86.9 _	AACgtgaat	74.7 _ *	-14 %