SYNGAP1[gene] - ClinVar - NCBI

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	Variation	Gene (Protein Change)	Type (Consequence)	Condition	Classification, Review status
Select item 155430	GRCh38/hg38 6p25.3-12.3(chr6:156974-46789291)x3	ILRUN-AS1, IP6K3 +2582 more	Copy number gain	See cases	GPathogenic
Select item 660703	NC_000006.11:g.(?_33131435)_(33419703_?)dup	B3GALT4, COL11A2 +26 more	Duplication	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 152279	GRCh38/hg38 6p21.32(chr6:33415354-33432929)x3	CUTA, PHF1 +1 more	Copy number gain	See cases	GUncertain significance
Select item 3079031	NM_001014433.2(CUTA):c.4A>T (p.Ile2Leu)	CUTA, SYNGAP1 (I2L)	Single nucleotide variant (missense variant)	not specified	GUncertain significance
Select item 1204001	NC_000006.12:g.33419822G>C	SYNGAP1	Single nucleotide variant	not provided	GLikely benign
Select item 1211719	NC_000006.12:g.33419836C>A	SYNGAP1	Single nucleotide variant	not provided	GLikely benign
Select item 1704830	NM_006772.3(SYNGAP1):c.-1G>A	SYNGAP1	Single nucleotide variant (5 prime UTR variant)	not provided	GUncertain significance
Select item 833646	NM_006772.3(SYNGAP1):c.3G>A (p.Met1Ile)	SYNGAP1 (M1I)	Single nucleotide variant (missense variant +1 more)	Inborn genetic diseases +2 more	GConflicting classifications of pathogenicity
Select item 1491962	NM_006772.3(SYNGAP1):c.5G>A (p.Ser2Asn)	SYNGAP1 (S2N)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5 +1 more	GUncertain significance
Select item 2750948	NM_006772.3(SYNGAP1):c.13C>G (p.Arg5Gly)	SYNGAP1 (R5G)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 2499008	NM_006772.3(SYNGAP1):c.14_27dup (p.Arg10fs)	SYNGAP1 (R10fs)	Duplication (frameshift variant)	not provided	GPathogenic
Select item 1304065	NM_006772.3(SYNGAP1):c.13C>T (p.Arg5Ter)	SYNGAP1 (R5*)	Single nucleotide variant (nonsense)	not provided	GUncertain significance
Select item 2808095	NM_006772.3(SYNGAP1):c.28del (p.Arg10fs)	SYNGAP1 (R10fs)	Deletion (frameshift variant)	Intellectual disability, autosomal dominant 5	GPathogenic
Select item 1254556	NM_006772.3(SYNGAP1):c.28C>T (p.Arg10Trp)	SYNGAP1 (R10W)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 1008683	NM_006772.3(SYNGAP1):c.28C>A (p.Arg10=)	SYNGAP1	Single nucleotide variant (synonymous variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 2995669	NM_006772.3(SYNGAP1):c.29G>A (p.Arg10Gln)	SYNGAP1 (R10Q)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 1020054	NM_006772.3(SYNGAP1):c.29G>C (p.Arg10Pro)	SYNGAP1 (R10P)	Single nucleotide variant (missense variant)	not provided +1 more	GUncertain significance
Select item 809919	NM_006772.3(SYNGAP1):c.33G>T (p.Gly11=)	SYNGAP1	Single nucleotide variant (synonymous variant)	Intellectual disability, autosomal dominant 5 +1 more	GLikely benign
Select item 537007	NM_006772.3(SYNGAP1):c.33G>A (p.Gly11=)	SYNGAP1	Single nucleotide variant (synonymous variant)	not provided +2 more	GLikely benign
Select item 495269	NM_006772.3(SYNGAP1):c.34_35del (p.Ser12fs)	SYNGAP1 (S12fs)	Deletion (frameshift variant)	Intellectual disability, autosomal dominant 5	GLikely pathogenic
Select item 1962619	NM_006772.3(SYNGAP1):c.36C>G (p.Ser12Arg)	SYNGAP1 (S12R)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 1155277	NM_006772.3(SYNGAP1):c.36C>T (p.Ser12=)	SYNGAP1	Single nucleotide variant (synonymous variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 1925632	NM_006772.3(SYNGAP1):c.43G>A (p.Ala15Thr)	SYNGAP1 (A15T)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 521836	NM_006772.3(SYNGAP1):c.43del (p.Ala15fs)	SYNGAP1 (A15fs)	Deletion (frameshift variant)	Inborn genetic diseases	GPathogenic
Select item 1801174	NM_006772.3(SYNGAP1):c.44C>T (p.Ala15Val)	SYNGAP1 (A15V)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 2838895	NM_006772.3(SYNGAP1):c.45G>C (p.Ala15=)	SYNGAP1	Single nucleotide variant (synonymous variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 537024	NM_006772.3(SYNGAP1):c.45G>A (p.Ala15=)	SYNGAP1	Single nucleotide variant (synonymous variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 1424213	NM_006772.3(SYNGAP1):c.48G>A (p.Met16Ile)	SYNGAP1 (M16I)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 1147915	NM_006772.3(SYNGAP1):c.51C>T (p.Ser17=)	SYNGAP1	Single nucleotide variant (synonymous variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 1967233	NM_006772.3(SYNGAP1):c.53A>G (p.Tyr18Cys)	SYNGAP1 (Y18C)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 469161	NM_006772.3(SYNGAP1):c.57C>T (p.Ala19=)	SYNGAP1	Single nucleotide variant (synonymous variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 1185912	NM_006772.3(SYNGAP1):c.59C>T (p.Pro20Leu)	SYNGAP1 (P20L)	Single nucleotide variant (missense variant)	not provided +1 more	GUncertain significance
Select item 566521	NM_006772.3(SYNGAP1):c.59C>G (p.Pro20Arg)	SYNGAP1 (P20R)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 813785	NM_006772.3(SYNGAP1):c.67+1G>T	SYNGAP1	Single nucleotide variant (splice donor variant)	Intellectual disability, autosomal dominant 5	GPathogenic
Select item 2436910	NM_006772.3(SYNGAP1):c.67+3A>C	SYNGAP1	Single nucleotide variant (intron variant)	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 2769122	NM_006772.3(SYNGAP1):c.67+9dup	SYNGAP1	Duplication (intron variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 1111806	NM_006772.3(SYNGAP1):c.67+9T>G	SYNGAP1	Single nucleotide variant (intron variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 537014	NM_006772.3(SYNGAP1):c.67+15del	SYNGAP1	Deletion (intron variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 2964434	NM_006772.3(SYNGAP1):c.67+13G>A	SYNGAP1	Single nucleotide variant (intron variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 2421978	NM_006772.3(SYNGAP1):c.67+15G>A	SYNGAP1	Single nucleotide variant (intron variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 1592860	NM_006772.3(SYNGAP1):c.67+16A>T	SYNGAP1	Single nucleotide variant (intron variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 1499588	NM_006772.3(SYNGAP1):c.67+20G>T	SYNGAP1	Single nucleotide variant (intron variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 1193956	NM_006772.3(SYNGAP1):c.67+186G>A	SYNGAP1	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 1185783	NM_006772.3(SYNGAP1):c.68-277C>G	SYNGAP1	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 1246549	NM_006772.3(SYNGAP1):c.68-79T>G	SYNGAP1	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 1227344	NM_006772.3(SYNGAP1):c.68-76C>T	SYNGAP1	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 1555985	NM_006772.3(SYNGAP1):c.68-19G>T	SYNGAP1	Single nucleotide variant (intron variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 3004622	NM_006772.3(SYNGAP1):c.68-15G>A	SYNGAP1	Single nucleotide variant (intron variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 2003351	NM_006772.3(SYNGAP1):c.68-3C>T	SYNGAP1	Single nucleotide variant (intron variant)	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 624242	NM_006772.3(SYNGAP1):c.68-1G>A	SYNGAP1	Single nucleotide variant (splice acceptor variant)	Intellectual disability, autosomal dominant 5 +1 more	GPathogenic/Likely pathogenic
Select item 2993054	NM_006772.3(SYNGAP1):c.73C>T (p.Arg25Trp)	SYNGAP1 (R25W)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 2598005	NM_006772.3(SYNGAP1):c.74G>A (p.Arg25Gln)	SYNGAP1 (R25Q)	Single nucleotide variant (missense variant)	Inborn genetic diseases	GUncertain significance
Select item 1133635	NM_006772.3(SYNGAP1):c.75G>T (p.Arg25=)	SYNGAP1	Single nucleotide variant (synonymous variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 1521495	NM_006772.3(SYNGAP1):c.76G>A (p.Gly26Arg)	SYNGAP1 (G26R)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5	GBenign
Select item 1553670	NM_006772.3(SYNGAP1):c.78A>C (p.Gly26=)	SYNGAP1	Single nucleotide variant (synonymous variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 1500161	NM_006772.3(SYNGAP1):c.82T>C (p.Ser28Pro)	SYNGAP1 (S28P)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 1806009	NM_006772.3(SYNGAP1):c.85_86del (p.Met29fs)	SYNGAP1 (M29fs)	Deletion (frameshift variant)	Intellectual disability, autosomal dominant 5	GPathogenic
Select item 130531	NM_006772.3(SYNGAP1):c.84T>C (p.Ser28=)	SYNGAP1	Single nucleotide variant (synonymous variant)	not provided +4 more	GBenign/Likely benign
Select item 1016030	NM_006772.3(SYNGAP1):c.86T>C (p.Met29Thr)	SYNGAP1 (M29T)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 972248	NM_006772.3(SYNGAP1):c.88C>T (p.His30Tyr)	SYNGAP1 (H30Y)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 1070521	NM_006772.3(SYNGAP1):c.91C>T (p.Arg31Ter)	SYNGAP1 (R31*)	Single nucleotide variant (nonsense)	Intellectual disability, autosomal dominant 5	GPathogenic
Select item 1977609	NM_006772.3(SYNGAP1):c.92G>A (p.Arg31Gln)	SYNGAP1 (R31Q)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 1699142	NM_006772.3(SYNGAP1):c.99del (p.Gln33fs)	SYNGAP1 (Q33fs)	Deletion (frameshift variant)	Intellectual disability, autosomal dominant 5	GPathogenic
Select item 1695865	NM_006772.3(SYNGAP1):c.102C>A (p.Tyr34Ter)	SYNGAP1 (Y34*)	Single nucleotide variant (nonsense)	not provided	GLikely pathogenic
Select item 469143	NM_006772.3(SYNGAP1):c.102C>T (p.Tyr34=)	SYNGAP1	Single nucleotide variant (synonymous variant)	Inborn genetic diseases +2 more	GBenign/Likely benign
Select item 2089635	NM_006772.3(SYNGAP1):c.106C>T (p.His36Tyr)	SYNGAP1 (H36Y)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 855079	NM_006772.3(SYNGAP1):c.113C>T (p.Pro38Leu)	SYNGAP1 (P38L)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5 +1 more	GConflicting classifications of pathogenicity
Select item 1105266	NM_006772.3(SYNGAP1):c.114G>T (p.Pro38=)	SYNGAP1	Single nucleotide variant (synonymous variant)	Intellectual disability, autosomal dominant 5 +1 more	GLikely benign
Select item 700155	NM_006772.3(SYNGAP1):c.114G>A (p.Pro38=)	SYNGAP1	Single nucleotide variant (synonymous variant)	Inborn genetic diseases +1 more	GLikely benign
Select item 2713431	NM_006772.3(SYNGAP1):c.117T>G (p.Tyr39Ter)	SYNGAP1 (Y39*)	Single nucleotide variant (nonsense)	Intellectual disability, autosomal dominant 5	GPathogenic
Select item 570959	NM_006772.3(SYNGAP1):c.121C>T (p.Arg41Cys)	SYNGAP1 (R41C)	Single nucleotide variant (missense variant)	not provided +2 more	GConflicting classifications of pathogenicity
Select item 1805923	NM_006772.3(SYNGAP1):c.123del (p.Pro42fs)	SYNGAP1 (P42fs)	Deletion (frameshift variant)	Intellectual disability, autosomal dominant 5	GPathogenic
Select item 1029086	NM_006772.3(SYNGAP1):c.127G>A (p.Gly43Ser)	SYNGAP1 (G43S)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 3323943	NM_006772.3(SYNGAP1):c.136C>T (p.Pro46Ser)	SYNGAP1 (P46S)	Single nucleotide variant (missense variant)	Inborn genetic diseases	GUncertain significance
Select item 436920	NM_006772.3(SYNGAP1):c.140G>A (p.Arg47Gln)	SYNGAP1 (R47Q)	Single nucleotide variant (missense variant)	not specified	GLikely benign
Select item 1510724	NM_006772.3(SYNGAP1):c.155C>T (p.Ser52Leu)	SYNGAP1 (S52L)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 436921	NM_006772.3(SYNGAP1):c.156G>A (p.Ser52=)	SYNGAP1	Single nucleotide variant (synonymous variant)	Intellectual disability, autosomal dominant 5 +1 more	GConflicting classifications of pathogenicity
Select item 520688	NM_006772.3(SYNGAP1):c.163C>A (p.Gln55Lys)	SYNGAP1 (Q55K)	Single nucleotide variant (missense variant)	Inborn genetic diseases +1 more	GUncertain significance
Select item 416787	NM_006772.3(SYNGAP1):c.166C>T (p.Leu56=)	SYNGAP1	Single nucleotide variant (synonymous variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 1973575	NM_006772.3(SYNGAP1):c.169C>T (p.Leu57Phe)	SYNGAP1 (L57F)	Single nucleotide variant (missense variant)	not provided +1 more	GUncertain significance
Select item 2962156	NM_006772.3(SYNGAP1):c.172A>G (p.Met58Val)	SYNGAP1 (M58V)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 2787948	NM_006772.3(SYNGAP1):c.175C>T (p.Leu59=)	SYNGAP1	Single nucleotide variant (synonymous variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 1646160	NC_000006.12:g.33423588ATGAGG[3]	SYNGAP1	Microsatellite	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 2830630	NM_006772.3(SYNGAP1):c.187G>A (p.Glu63Lys)	SYNGAP1 (E63K)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 2132335	NM_006772.3(SYNGAP1):c.187G>C (p.Glu63Gln)	SYNGAP1 (E63Q)	Single nucleotide variant (missense variant)	Intellectual disability, autosomal dominant 5	GUncertain significance
Select item 2863711	NM_006772.3(SYNGAP1):c.189+1G>A	SYNGAP1	Single nucleotide variant (splice donor variant)	Intellectual disability, autosomal dominant 5	GLikely pathogenic
Select item 1970525	NM_006772.3(SYNGAP1):c.189+8_189+9del	SYNGAP1	Microsatellite (intron variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 1591857	NM_006772.3(SYNGAP1):c.189+15_189+16delinsGC	SYNGAP1	Indel (intron variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 1961584	NM_006772.3(SYNGAP1):c.189+18G>C	SYNGAP1	Single nucleotide variant (intron variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 1266996	NM_006772.3(SYNGAP1):c.189+29G>A	SYNGAP1	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 1197249	NM_006772.3(SYNGAP1):c.190-148A>G	SYNGAP1	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 1249713	NM_006772.3(SYNGAP1):c.190-50G>A	SYNGAP1	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 1582432	NM_006772.3(SYNGAP1):c.190-12del	SYNGAP1	Deletion (intron variant)	Intellectual disability, autosomal dominant 5	GBenign
Select item 1567783	NM_006772.3(SYNGAP1):c.190-16C>T	SYNGAP1	Single nucleotide variant (intron variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 2896503	NM_006772.3(SYNGAP1):c.190-14C>T	SYNGAP1	Single nucleotide variant (intron variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 2768097	NM_006772.3(SYNGAP1):c.190-12C>G	SYNGAP1	Single nucleotide variant (intron variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 1105529	NM_006772.3(SYNGAP1):c.190-8T>C	SYNGAP1	Single nucleotide variant (intron variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 1130414	NM_006772.3(SYNGAP1):c.190-7C>T	SYNGAP1	Single nucleotide variant (intron variant)	Intellectual disability, autosomal dominant 5	GLikely benign
Select item 1075175	NM_006772.3(SYNGAP1):c.190-2A>C	SYNGAP1	Single nucleotide variant (splice acceptor variant)	Intellectual disability, autosomal dominant 5	GPathogenic
Select item 951934	NM_006772.3(SYNGAP1):c.190-2A>G	SYNGAP1	Single nucleotide variant (splice acceptor variant)	Intellectual disability, autosomal dominant 5	GPathogenic

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