SCN2A[gene] - ClinVar - NCBI

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	Variation	Gene (Protein Change)	Type (Consequence)	Condition	Classification, Review status
Select item 154177	GRCh38/hg38 2q24.1-31.1(chr2:154294042-175989372)x3	ABCB11, ACVR1 +532 more	Copy number gain	See cases	GPathogenic
Select item 59150	GRCh38/hg38 2q24.1-24.3(chr2:154366788-167048902)x3	GALNT3, GALNT5 +275 more	Copy number gain	See cases	GPathogenic
Select item 57318	GRCh38/hg38 2q24.1-24.3(chr2:158382388-166605758)x1	BAZ2B, BAZ2B-AS1 +197 more	Copy number loss	See cases	GPathogenic
Select item 148507	GRCh38/hg38 2q24.3(chr2:163419387-165682938)x1	COBLL1, CSRNP3 +26 more	Copy number loss	See cases	GLikely pathogenic
Select item 60245	GRCh38/hg38 2q24.3(chr2:163455290-166962322)x1	COBLL1, CSRNP3 +38 more	Copy number loss	See cases	GPathogenic
Select item 60248	GRCh38/hg38 2q24.3-32.1(chr2:163965382-182195062)x1	CFAP210, ABCB11 +491 more	Copy number loss	See cases	GPathogenic
Select item 60249	GRCh38/hg38 2q24.3-31.1(chr2:164066038-172097886)x1	ABCB11, B3GALT1 +163 more	Copy number loss	See cases	GPathogenic
Select item 57491	GRCh38/hg38 2q24.3-31.1(chr2:164850117-175559190)x1	LOC129935095, LOC129935096 +271 more	Copy number loss	See cases	GPathogenic
Select item 144471	GRCh38/hg38 2q24.3(chr2:164920562-167536439)x3	B3GALT1, CSRNP3 +25 more	Copy number gain	See cases	GPathogenic
Select item 153729	GRCh38/hg38 2q24.3(chr2:164941760-165764726)x3	CSRNP3, GALNT3 +9 more	Copy number gain	See cases	GLikely pathogenic
Select item 1707403	GRCh38/hg38 2q24.3(chr2:165155128-166062451)x1	LOC126806396, CSRNP3 +15 more	Copy number loss	Epilepsy of infancy with migrating focal seizures	GPathogenic
Select item 652948	NC_000002.12:g.(?_165090130)_(166286643_?)del	LOC129935045, LOC129935046 +17 more	Deletion	Developmental and epileptic encephalopathy +2 more	GPathogenic
Select item 651833	NC_000002.12:g.(?_165090130)_(166311776_?)del	SCN1A-AS1, SCN2A +17 more	Deletion	Developmental and epileptic encephalopathy	GPathogenic
Select item 533507	NC_000002.11:g.(?_165946640)_(166246354_?)dup	LOC120977013, LOC129935043 +2 more	Duplication	Seizures, benign familial infantile, 3 +1 more	GUncertain significance
Select item 530654	NC_000002.12:g.(?_165090130)_(166228992_?)del	CSRNP3, GALNT3 +17 more	Deletion	Neuropathy, hereditary sensory and autonomic, type 2A +2 more	GPathogenic
Select item 584355	NC_000002.11:g.(?_165946660)_(166246334_?)dup	LOC120977013, LOC129935043 +2 more	Duplication	Developmental and epileptic encephalopathy, 11 +1 more	GUncertain significance
Select item 155321	GRCh38/hg38 2q24.3(chr2:165222998-166664612)x1	CSRNP3, GALNT3 +16 more	Copy number loss	See cases	GPathogenic
Select item 153359	GRCh38/hg38 2q24.3(chr2:165238425-166114982)x1	CSRNP3, GALNT3 +14 more	Copy number loss	See cases	GPathogenic
Select item 1707404	GRCh38/hg38 2q24.3(chr2:165383106-167432622)x1	B3GALT1, CSRNP3 +22 more	Copy number loss	West syndrome	GPathogenic
Select item 1245138	NM_001040142.2(SCN2A):c.-51-1983G>C	LOC120977013, SCN2A	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 331704	NM_001040142.2(SCN2A):c.-51-1925G>A	LOC120977013, SCN2A	Single nucleotide variant (intron variant)	Seizures, benign familial infantile, 3	GUncertain significance
Select item 331705	NM_001040142.2(SCN2A):c.-51-1914C>T	LOC120977013, SCN2A	Single nucleotide variant (intron variant)	Seizures, benign familial infantile, 3	GUncertain significance
Select item 331707	NM_001040142.2(SCN2A):c.-51-1737_-51-1735dup	LOC120977013, SCN2A	Duplication (intron variant)	Early Infantile Epileptic Encephalopathy, Autosomal Dominant +2 more	GUncertain significance
Select item 331706	NM_001040142.2(SCN2A):c.-51-1736_-51-1735dup	LOC120977013, SCN2A	Duplication (intron variant)	Early Infantile Epileptic Encephalopathy, Autosomal Dominant +2 more	GConflicting classifications of pathogenicity
Select item 1703351	NM_001040142.2(SCN2A):c.-51-1737_-51-1735del	LOC120977013, SCN2A	Deletion (intron variant)	not provided	GLikely benign
Select item 894299	NM_001040142.2(SCN2A):c.-51-1762A>T	LOC120977013, SCN2A	Single nucleotide variant (intron variant)	Seizures, benign familial infantile, 3	GUncertain significance
Select item 331709	NM_001040142.2(SCN2A):c.-51-1736_-51-1735del	LOC120977013, SCN2A	Deletion (intron variant)	Episodic ataxia, type 9 +3 more	GConflicting classifications of pathogenicity
Select item 331708	NM_001040142.2(SCN2A):c.-51-1735del	LOC120977013, SCN2A	Deletion (intron variant)	Episodic ataxia, type 9 +3 more	GConflicting classifications of pathogenicity
Select item 894300	NM_001040142.2(SCN2A):c.-51-1758A>C	LOC120977013, SCN2A	Single nucleotide variant (intron variant)	Seizures, benign familial infantile, 3	GUncertain significance
Select item 331710	NM_001040142.2(SCN2A):c.-51-1735_-51-1733del	SCN2A	Deletion (intron variant)	Seizures, benign familial infantile, 3 +1 more	GUncertain significance
Select item 331711	NM_001040142.2(SCN2A):c.-51-1734_-51-1733del	SCN2A	Deletion (intron variant)	Seizures, benign familial infantile, 3 +1 more	GUncertain significance
Select item 331715	NM_001040142.2(SCN2A):c.-51-1733_-51-1732insAA	SCN2A	Insertion (intron variant)	Early Infantile Epileptic Encephalopathy, Autosomal Dominant +1 more	GUncertain significance
Select item 331714	NM_001040142.2(SCN2A):c.-51-1733_-51-1732dup	SCN2A	Duplication (intron variant)	Early Infantile Epileptic Encephalopathy, Autosomal Dominant +1 more	GUncertain significance
Select item 331713	NM_001040142.2(SCN2A):c.-51-1734G>A	SCN2A	Single nucleotide variant (intron variant)	Seizures, benign familial infantile, 3	GUncertain significance
Select item 331712	NM_001040142.2(SCN2A):c.-51-1734del	SCN2A	Deletion (intron variant)	Early Infantile Epileptic Encephalopathy, Autosomal Dominant +1 more	GUncertain significance
Select item 2651482	NM_001040142.2(SCN2A):c.-51-1722_-51-1720dup	SCN2A	Duplication (intron variant)	not provided	GBenign
Select item 892840	NM_001040142.2(SCN2A):c.-51-1733A>T	SCN2A	Single nucleotide variant (intron variant)	Seizures, benign familial infantile, 3	GUncertain significance
Select item 331724	NM_001040142.2(SCN2A):c.-51-1721_-51-1720dup	SCN2A	Duplication (intron variant)	Seizures, benign familial infantile, 3 +2 more	GUncertain significance
Select item 331723	NM_001040142.2(SCN2A):c.-51-1720dup	SCN2A	Duplication (intron variant)	Seizures, benign familial infantile, 3 +2 more	GUncertain significance
Select item 331722	NM_001040142.2(SCN2A):c.-51-1733_-51-1732insGATT	SCN2A	Insertion (intron variant)	Seizures, benign familial infantile, 3 +1 more	GUncertain significance
Select item 331721	NM_001040142.2(SCN2A):c.-51-1733_-51-1732insGAT	SCN2A	Insertion (intron variant)	Seizures, benign familial infantile, 3 +1 more	GUncertain significance
Select item 331720	NM_001040142.2(SCN2A):c.-51-1733_-51-1732insAGATT	SCN2A	Insertion (intron variant)	Seizures, benign familial infantile, 3 +1 more	GUncertain significance
Select item 331719	NM_001040142.2(SCN2A):c.-51-1733_-51-1732insAATTT	SCN2A	Insertion (intron variant)	Seizures, benign familial infantile, 3 +1 more	GUncertain significance
Select item 331718	NM_001040142.2(SCN2A):c.-51-1733_-51-1732insAATT	SCN2A	Insertion (intron variant)	Seizures, benign familial infantile, 3 +1 more	GUncertain significance
Select item 331717	NM_001040142.2(SCN2A):c.-51-1733_-51-1732insAAT	SCN2A	Insertion (intron variant)	Early Infantile Epileptic Encephalopathy, Autosomal Dominant +1 more	GUncertain significance
Select item 331716	NM_001040142.2(SCN2A):c.-51-1733_-51-1732insAAAT	SCN2A	Insertion (intron variant)	Early Infantile Epileptic Encephalopathy, Autosomal Dominant +1 more	GUncertain significance
Select item 331725	NM_001040142.2(SCN2A):c.-51-1729T>C	SCN2A	Single nucleotide variant (intron variant)	Seizures, benign familial infantile, 3	GUncertain significance
Select item 206959	NM_001040142.2(SCN2A):c.-51-1658G>T	SCN2A	Single nucleotide variant (5 prime UTR variant +1 more)	not specified	GLikely benign
Select item 507166	NM_001040142.2(SCN2A):c.-51-1657G>T	SCN2A	Single nucleotide variant (5 prime UTR variant +1 more)	not specified	GLikely benign
Select item 331726	NM_001040142.2(SCN2A):c.-51-1652A>G	SCN2A	Single nucleotide variant (5 prime UTR variant +1 more)	Seizures, benign familial infantile, 3	GUncertain significance
Select item 2579570	NM_001040142.2(SCN2A):c.-51-1637G>T	SCN2A	Single nucleotide variant (intron variant +1 more)	not provided	GUncertain significance
Select item 1227407	NM_001040142.2(SCN2A):c.-51-172T>C	SCN2A	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 677402	NM_001040142.2(SCN2A):c.-51-136C>T	SCN2A	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 1220984	NM_001040142.2(SCN2A):c.-51-98A>G	SCN2A	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 670920	NM_001040142.2(SCN2A):c.-51-61A>G	SCN2A	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 419944	NM_001040142.2(SCN2A):c.-51-16dup	SCN2A	Duplication (intron variant)	not provided	GLikely benign
Select item 495276	NC_000002.11:g.(?_166152283)_(166246384_?)dup	SCN2A	Duplication	Seizures, benign familial infantile, 3	GLikely pathogenic
Select item 892841	NM_001040142.2(SCN2A):c.-42A>C	SCN2A	Single nucleotide variant (5 prime UTR variant)	Seizures, benign familial infantile, 3	GUncertain significance
Select item 515669	NM_001040142.2(SCN2A):c.-41T>C	SCN2A	Single nucleotide variant (5 prime UTR variant)	not specified	GLikely benign
Select item 655230	NC_000002.11:g.(?_166152314)_(167108415_?)dup	LOC129935046, LOC129935047 +14 more	Duplication	Developmental and epileptic encephalopathy +2 more	GUncertain significance
Select item 559888	NM_001040142.2(SCN2A):c.1A>T (p.Met1Leu)	SCN2A (M1L)	Single nucleotide variant (missense variant +1 more)	Developmental and epileptic encephalopathy, 11	GLikely pathogenic
Select item 3760265	NM_001040142.2(SCN2A):c.3G>A (p.Met1Ile)	SCN2A (M1I)	Single nucleotide variant (missense variant +1 more)	Seizures, benign familial infantile, 3 +1 more	GPathogenic
Select item 962441	NM_001040142.2(SCN2A):c.7C>T (p.Gln3Ter)	SCN2A (Q3*)	Single nucleotide variant (nonsense)	Seizures, benign familial infantile, 3 +1 more	GPathogenic
Select item 2922489	NM_001040142.2(SCN2A):c.8A>G (p.Gln3Arg)	SCN2A (Q3R)	Single nucleotide variant (missense variant)	Seizures, benign familial infantile, 3 +1 more	GUncertain significance
Select item 2307995	NM_001040142.2(SCN2A):c.9G>C (p.Gln3His)	SCN2A (Q3H)	Single nucleotide variant (missense variant)	Inborn genetic diseases	GUncertain significance
Select item 1135330	NM_001040142.2(SCN2A):c.9G>A (p.Gln3=)	SCN2A	Single nucleotide variant (synonymous variant)	Developmental and epileptic encephalopathy, 11 +1 more	GLikely benign
Select item 436659	NM_001040142.2(SCN2A):c.11C>G (p.Ser4Ter)	SCN2A (S4*)	Single nucleotide variant (nonsense)	Developmental and epileptic encephalopathy, 11	GPathogenic
Select item 1994395	NM_001040142.2(SCN2A):c.12A>G (p.Ser4=)	SCN2A	Single nucleotide variant (synonymous variant)	Seizures, benign familial infantile, 3 +1 more	GLikely benign
Select item 2941800	NM_001040142.2(SCN2A):c.13G>A (p.Val5Met)	SCN2A (V5M)	Single nucleotide variant (missense variant)	Seizures, benign familial infantile, 3 +1 more	GUncertain significance
Select item 1709970	NM_001040142.2(SCN2A):c.16C>A (p.Leu6Met)	SCN2A (L6M)	Single nucleotide variant (missense variant)	Developmental and epileptic encephalopathy, 11	GUncertain significance
Select item 994753	NM_001040142.2(SCN2A):c.23C>A (p.Pro8Gln)	SCN2A (P8Q)	Single nucleotide variant (missense variant)	Developmental and epileptic encephalopathy, 11 +2 more	GUncertain significance
Select item 207031	NM_001040142.2(SCN2A):c.23C>T (p.Pro8Leu)	SCN2A (P8L)	Single nucleotide variant (missense variant)	Seizures, benign familial infantile, 3 +2 more	GUncertain significance
Select item 2932289	NM_001040142.2(SCN2A):c.24G>T (p.Pro8=)	SCN2A	Single nucleotide variant (synonymous variant)	Seizures, benign familial infantile, 3 +1 more	GLikely benign
Select item 139022	NM_001040142.2(SCN2A):c.24G>A (p.Pro8=)	SCN2A	Single nucleotide variant (synonymous variant)	Inborn genetic diseases +4 more	GConflicting classifications of pathogenicity
Select item 1154638	NM_001040142.2(SCN2A):c.27A>T (p.Pro9=)	SCN2A	Single nucleotide variant (synonymous variant)	Developmental and epileptic encephalopathy, 11 +1 more	GLikely benign
Select item 1320412	NM_001040142.2(SCN2A):c.31C>G (p.Pro11Ala)	SCN2A (P11A)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 3764205	NM_001040142.2(SCN2A):c.32C>T (p.Pro11Leu)	SCN2A (P11L)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 1727249	NM_001040142.2(SCN2A):c.34G>A (p.Asp12Asn)	SCN2A (D12N)	Single nucleotide variant (missense variant)	Not Specified
Select item 3793186	NM_001040142.2(SCN2A):c.36C>A (p.Asp12Glu)	SCN2A (D12E)	Single nucleotide variant (missense variant)	Inborn genetic diseases	GUncertain significance
Select item 1625280	NM_001040142.2(SCN2A):c.36C>T (p.Asp12=)	SCN2A	Single nucleotide variant (synonymous variant)	Developmental and epileptic encephalopathy, 11 +1 more	GLikely benign
Select item 833625	NM_001040142.2(SCN2A):c.36C>G (p.Asp12Glu)	SCN2A (D12E)	Single nucleotide variant (missense variant)	Seizures, benign familial infantile, 3 +1 more	GLikely benign
Select item 1317212	NM_001040142.2(SCN2A):c.37A>G (p.Ser13Gly)	SCN2A (S13G)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 2651483	NM_001040142.2(SCN2A):c.43C>T (p.Arg15Cys)	SCN2A (R15C)	Single nucleotide variant (missense variant)	not provided +2 more	GConflicting classifications of pathogenicity
Select item 2147500	NM_001040142.2(SCN2A):c.44G>A (p.Arg15His)	SCN2A (R15H)	Single nucleotide variant (missense variant)	Seizures, benign familial infantile, 3 +1 more	GLikely benign
Select item 1963264	NM_001040142.2(SCN2A):c.51T>C (p.Phe17=)	SCN2A	Single nucleotide variant (synonymous variant)	Seizures, benign familial infantile, 3 +1 more	GUncertain significance
Select item 130224	NM_001040142.2(SCN2A):c.56G>A (p.Arg19Lys)	SCN2A (R19K)	Single nucleotide variant (missense variant)	Complex neurodevelopmental disorder	GBenignFDA Recognized database
Select item 207032	NM_001040142.2(SCN2A):c.70G>A (p.Ala24Thr)	SCN2A (A24T)	Single nucleotide variant (missense variant)	Inborn genetic diseases +3 more	GBenign/Likely benign
Select item 1060840	NM_001040142.2(SCN2A):c.73A>G (p.Ile25Val)	SCN2A (I25V)	Single nucleotide variant (missense variant)	Seizures, benign familial infantile, 3 +1 more	GUncertain significance
Select item 1468971	NM_001040142.2(SCN2A):c.74T>C (p.Ile25Thr)	SCN2A (I25T)	Single nucleotide variant (missense variant)	Seizures, benign familial infantile, 3 +1 more	GUncertain significance
Select item 1318844	NM_001040142.2(SCN2A):c.74T>G (p.Ile25Ser)	SCN2A (I25S)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 1326533	NM_001040142.2(SCN2A):c.76G>C (p.Glu26Gln)	SCN2A (E26Q)	Single nucleotide variant (missense variant)	not provided +1 more	GUncertain significance
Select item 1508902	NM_001040142.2(SCN2A):c.81A>G (p.Gln27=)	SCN2A	Single nucleotide variant (synonymous variant)	Seizures, benign familial infantile, 3 +3 more	GConflicting classifications of pathogenicity
Select item 1318695	NM_001040142.2(SCN2A):c.81A>T (p.Gln27His)	SCN2A (Q27H)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 207033	NM_001040142.2(SCN2A):c.82C>T (p.Arg28Cys)	SCN2A (R28C)	Single nucleotide variant (missense variant)	Inborn genetic diseases +4 more	GBenign/Likely benign
Select item 3363670	NM_001040142.2(SCN2A):c.83G>T (p.Arg28Leu)	SCN2A (R28L)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 1878591	NM_001040142.2(SCN2A):c.83G>A (p.Arg28His)	SCN2A (R28H)	Single nucleotide variant (missense variant)	Seizures, benign familial infantile, 3 +1 more	GConflicting classifications of pathogenicity
Select item 574534	NM_001040142.2(SCN2A):c.88G>A (p.Ala30Thr)	SCN2A (A30T)	Single nucleotide variant (missense variant)	Developmental and epileptic encephalopathy, 11 +1 more	GUncertain significance
Select item 3366179	NM_001040142.2(SCN2A):c.89C>G (p.Ala30Gly)	SCN2A (A30G)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 2580091	NM_001040142.2(SCN2A):c.91G>A (p.Glu31Lys)	SCN2A (E31K)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 3753647	NM_001040142.2(SCN2A):c.94G>A (p.Glu32Lys)	SCN2A (E32K)	Single nucleotide variant (missense variant)	not provided +2 more	GUncertain significance

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