SPRED1[gene] - ClinVar - NCBI

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	Variation	Gene (Protein Change)	Type (Consequence)	Condition	Classification, Review status
Select item 149530	GRCh38/hg38 15q11.2-14(chr15:23319714-38545325)x3	ACTC1, APBA2 +363 more	Copy number gain	See cases	GPathogenic
Select item 57876	GRCh38/hg38 15q13.3-14(chr15:32326136-39394068)x1	LOC132090301, LOC132090302 +178 more	Copy number loss	See cases	GPathogenic
Select item 57877	GRCh38/hg38 15q13.3-15.1(chr15:32635803-40233825)x1	ACTC1, AQR +219 more	Copy number loss	See cases	GPathogenic
Select item 57878	GRCh38/hg38 15q14(chr15:34588015-39280404)x1	ACTC1, AQR +99 more	Copy number loss	See cases	GPathogenic
Select item 57226	GRCh38/hg38 15q14(chr15:34995451-39735062)x1	CDIN1, DPH6 +92 more	Copy number loss	See cases	GPathogenic
Select item 151932	GRCh38/hg38 15q14(chr15:38154297-38507355)x3	FAM98B, LOC125078059 +11 more	Copy number gain	See cases	GUncertain significance
Select item 1205162	NC_000015.10:g.38252630G>T	SPRED1	Single nucleotide variant (genic upstream transcript variant)	not provided	GLikely benign
Select item 1216131	NM_152594.3(SPRED1):c.-332G>A	SPRED1	Single nucleotide variant (5 prime UTR variant)	not provided	GLikely benign
Select item 315724	NM_152594.3(SPRED1):c.-309C>T	SPRED1	Single nucleotide variant (5 prime UTR variant)	Legius syndrome	GUncertain significance
Select item 631554	NM_152594.3(SPRED1):c.-294CT[2]	SPRED1	Microsatellite (5 prime UTR variant)	RASopathy	GLikely benign
Select item 315725	NM_152594.3(SPRED1):c.-294C>T	SPRED1	Single nucleotide variant (5 prime UTR variant)	Legius syndrome	GUncertain significance
Select item 315726	NM_152594.3(SPRED1):c.-244T>C	LOC130056788, SPRED1	Single nucleotide variant (5 prime UTR variant)	Legius syndrome	GBenign
Select item 315727	NM_152594.3(SPRED1):c.-201G>A	LOC130056788, SPRED1	Single nucleotide variant (5 prime UTR variant)	Legius syndrome	GUncertain significance
Select item 315728	NM_152594.3(SPRED1):c.-191C>T	SPRED1	Single nucleotide variant (5 prime UTR variant)	Legius syndrome	GLikely benign
Select item 886069	NM_152594.3(SPRED1):c.-175G>T	LOC130056789, SPRED1	Single nucleotide variant (5 prime UTR variant)	Legius syndrome	GUncertain significance
Select item 315729	NM_152594.3(SPRED1):c.-156del	LOC130056789, SPRED1	Deletion (5 prime UTR variant)	Legius syndrome	GLikely benign
Select item 315730	NM_152594.3(SPRED1):c.-152C>A	LOC130056789, SPRED1	Single nucleotide variant (5 prime UTR variant)	Legius syndrome	GUncertain significance
Select item 2505194	NM_152594.3(SPRED1):c.-134C>T	SPRED1	Single nucleotide variant (5 prime UTR variant)	not provided	GUncertain significance
Select item 886070	NM_152594.3(SPRED1):c.-114G>A	SPRED1	Single nucleotide variant (5 prime UTR variant)	Legius syndrome	GUncertain significance
Select item 315731	NM_152594.3(SPRED1):c.-93C>T	SPRED1	Single nucleotide variant (5 prime UTR variant)	Noonan syndrome and Noonan-related syndrome +2 more	GBenign
Select item 315732	NM_152594.3(SPRED1):c.-87C>T	SPRED1	Single nucleotide variant (5 prime UTR variant)	Legius syndrome	GUncertain significance
Select item 887069	NM_152594.3(SPRED1):c.-24A>G	SPRED1	Single nucleotide variant (5 prime UTR variant)	Legius syndrome	GUncertain significance
Select item 373016	NM_152594.3(SPRED1):c.-22A>C	SPRED1	Single nucleotide variant (5 prime UTR variant)	not specified	GUncertain significance
Select item 583432	NC_000015.10:g.(?_38253166)_(39021201_?)del	FAM98B, LINC02694 +24 more	Deletion	Legius syndrome	GPathogenic
Select item 504128	NM_152594.3(SPRED1):c.-18G>T	SPRED1	Single nucleotide variant (5 prime UTR variant)	not provided	GUncertain significance
Select item 928827	NM_152594.3(SPRED1):c.-12G>C	SPRED1	Single nucleotide variant (5 prime UTR variant)	not specified	GUncertain significance
Select item 229268	NM_152594.3(SPRED1):c.-12G>T	SPRED1	Single nucleotide variant (5 prime UTR variant)	not specified	GUncertain significance
Select item 584323	NC_000015.10:g.(?_38253180)_(38351670_?)del	LOC129390685, SPRED1	Deletion	Legius syndrome	GPathogenic
Select item 1334303	NM_152594.3(SPRED1):c.-2A>T	SPRED1	Single nucleotide variant (5 prime UTR variant)	Cardiovascular phenotype +1 more	GUncertain significance
Select item 3362511	NM_152594.3(SPRED1):c.1A>T (p.Met1Leu)	SPRED1 (M1L)	Single nucleotide variant (missense variant +1 more)	Legius syndrome	GLikely pathogenic
Select item 930640	NM_152594.3(SPRED1):c.1A>G (p.Met1Val)	SPRED1 (M1V)	Single nucleotide variant (missense variant +1 more)	Legius syndrome	GPathogenic/Likely pathogenic
Select item 547788	NM_152594.3(SPRED1):c.1_2del (p.Met1fs)	SPRED1 (M1fs)	Deletion (frameshift variant +1 more)	Legius syndrome	GLikely pathogenic
Select item 854050	NM_152594.3(SPRED1):c.3G>A (p.Met1Ile)	SPRED1 (M1I)	Single nucleotide variant (missense variant +1 more)	Legius syndrome	GPathogenic
Select item 965391	NM_152594.3(SPRED1):c.6C>A (p.Ser2Arg)	SPRED1 (S2R)	Single nucleotide variant (missense variant)	Cardiovascular phenotype +1 more	GUncertain significance
Select item 547789	NM_152594.3(SPRED1):c.7_20del (p.Glu3fs)	SPRED1 (E3fs)	Deletion (frameshift variant)	Legius syndrome	GPathogenic
Select item 1122281	NM_152594.3(SPRED1):c.9G>A (p.Glu3=)	SPRED1	Single nucleotide variant (synonymous variant)	Legius syndrome	GLikely benign
Select item 1309782	NM_152594.3(SPRED1):c.14C>G (p.Thr5Arg)	SPRED1 (T5R)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 1092673	NM_152594.3(SPRED1):c.15G>C (p.Thr5=)	SPRED1	Single nucleotide variant (synonymous variant)	Legius syndrome +2 more	GLikely benign
Select item 1417521	NM_152594.3(SPRED1):c.17C>G (p.Ala6Gly)	SPRED1 (A6G)	Single nucleotide variant (missense variant)	Legius syndrome	GUncertain significance
Select item 2997217	NM_152594.3(SPRED1):c.20C>T (p.Thr7Ile)	SPRED1 (T7I)	Single nucleotide variant (missense variant)	Legius syndrome	GUncertain significance
Select item 2059176	NM_152594.3(SPRED1):c.21T>A (p.Thr7=)	SPRED1	Single nucleotide variant (synonymous variant)	Legius syndrome	GLikely benign
Select item 547790	NM_152594.3(SPRED1):c.24del (p.Asp9fs)	SPRED1 (D9fs)	Deletion (frameshift variant)	Legius syndrome	GLikely pathogenic
Select item 2828445	NM_152594.3(SPRED1):c.25G>A (p.Asp9Asn)	SPRED1 (D9N)	Single nucleotide variant (missense variant)	Legius syndrome	GUncertain significance
Select item 47967	NM_152594.3(SPRED1):c.26A>T (p.Asp9Val)	SPRED1 (D9V)	Single nucleotide variant (missense variant)	Legius syndrome +4 more	GBenign/Likely benign
Select item 179219	NM_152594.3(SPRED1):c.27C>T (p.Asp9=)	SPRED1	Single nucleotide variant (synonymous variant)	not specified +1 more	GLikely benign
Select item 1978868	NM_152594.3(SPRED1):c.28A>G (p.Asn10Asp)	SPRED1 (N10D)	Single nucleotide variant (missense variant)	Cardiovascular phenotype +1 more	GUncertain significance
Select item 970869	NM_152594.3(SPRED1):c.29A>G (p.Asn10Ser)	SPRED1 (N10S)	Single nucleotide variant (missense variant)	Legius syndrome	GUncertain significance
Select item 415718	NM_152594.3(SPRED1):c.30C>A (p.Asn10Lys)	SPRED1 (N10K)	Single nucleotide variant (missense variant)	Noonan syndrome and Noonan-related syndrome +4 more	GBenign/Likely benign
Select item 966373	NM_152594.3(SPRED1):c.31G>A (p.Asp11Asn)	SPRED1 (D11N)	Single nucleotide variant (missense variant)	Legius syndrome	GUncertain significance
Select item 1341771	NM_152594.3(SPRED1):c.32A>T (p.Asp11Val)	SPRED1 (D11V)	Single nucleotide variant (missense variant)	Legius syndrome	GUncertain significance
Select item 3248543	NM_152594.3(SPRED1):c.32+2T>C	SPRED1	Single nucleotide variant (splice donor variant)	Neurofibromatosis, type 1	GLikely pathogenic
Select item 2914367	NM_152594.3(SPRED1):c.32+3_32+6dup	SPRED1	Duplication (intron variant)	Legius syndrome	GLikely benign
Select item 1510307	NM_152594.3(SPRED1):c.32+2T>G	SPRED1	Single nucleotide variant (splice donor variant)	Legius syndrome	GLikely pathogenic
Select item 1038674	NM_152594.3(SPRED1):c.32+3A>T	SPRED1	Single nucleotide variant (intron variant)	Legius syndrome	GUncertain significance
Select item 3014255	NM_152594.3(SPRED1):c.32+9C>T	SPRED1	Single nucleotide variant (intron variant)	Legius syndrome	GLikely benign
Select item 1957433	NM_152594.3(SPRED1):c.32+12A>G	SPRED1	Single nucleotide variant (intron variant)	Legius syndrome	GLikely benign
Select item 1609820	NM_152594.3(SPRED1):c.32+14T>C	SPRED1	Single nucleotide variant (intron variant)	Legius syndrome	GLikely benign
Select item 2702911	NM_152594.3(SPRED1):c.32+18C>G	SPRED1	Single nucleotide variant (intron variant)	Legius syndrome	GLikely benign
Select item 2176947	NM_152594.3(SPRED1):c.32+18C>T	SPRED1	Single nucleotide variant (intron variant)	Legius syndrome	GLikely benign
Select item 984457	NM_152594.3(SPRED1):c.32+20C>T	SPRED1	Single nucleotide variant (intron variant)	Legius syndrome +1 more	GBenign
Select item 1208134	NM_152594.3(SPRED1):c.32+162G>A	SPRED1	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 561829	NM_152594.3(SPRED1):c.32+307A>C	SPRED1	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 561830	NM_152594.3(SPRED1):c.33-274A>G	SPRED1	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 3022147	NM_152594.3(SPRED1):c.33-14T>C	SPRED1	Single nucleotide variant (intron variant)	Legius syndrome	GLikely benign
Select item 511367	NM_152594.3(SPRED1):c.33-11A>G	SPRED1	Single nucleotide variant (intron variant)	Legius syndrome +1 more	GLikely benign
Select item 415720	NM_152594.3(SPRED1):c.33-7A>G	SPRED1	Single nucleotide variant (intron variant)	Legius syndrome	GLikely benign
Select item 1298611	NM_152594.3(SPRED1):c.33-1G>A	SPRED1	Single nucleotide variant (splice acceptor variant)	not provided +1 more	GLikely pathogenic
Select item 417474	NC_000015.10:g.(?_38299373)_(38357249_?)del	SPRED1	Deletion	Legius syndrome	GPathogenic
Select item 372680	NM_152594.3(SPRED1):c.38G>A (p.Ser13Asn)	SPRED1 (S13N)	Single nucleotide variant (missense variant)	not specified	GUncertain significance
Select item 1638223	NM_152594.3(SPRED1):c.39T>C (p.Ser13=)	SPRED1	Single nucleotide variant (synonymous variant)	Legius syndrome	GLikely benign
Select item 1386579	NM_152594.3(SPRED1):c.40del (p.Tyr14fs)	SPRED1 (Y14fs)	Deletion (frameshift variant)	Legius syndrome	GPathogenic
Select item 3337631	NM_152594.3(SPRED1):c.42T>A (p.Tyr14Ter)	SPRED1 (Y14*)	Single nucleotide variant (nonsense)	not provided	GLikely pathogenic
Select item 2825380	NM_152594.3(SPRED1):c.42T>G (p.Tyr14Ter)	SPRED1 (Y14*)	Single nucleotide variant (nonsense)	Legius syndrome	GPathogenic
Select item 1177280	NM_152594.3(SPRED1):c.42T>C (p.Tyr14=)	SPRED1	Single nucleotide variant (synonymous variant)	Cardiovascular phenotype +2 more	GConflicting classifications of pathogenicity
Select item 1334304	NM_152594.3(SPRED1):c.43G>A (p.Ala15Thr)	SPRED1 (A15T)	Single nucleotide variant (missense variant)	Cardiovascular phenotype +1 more	GUncertain significance
Select item 2139826	NM_152594.3(SPRED1):c.46C>G (p.Arg16Gly)	SPRED1 (R16G)	Single nucleotide variant (missense variant)	Legius syndrome	GUncertain significance
Select item 372718	NM_152594.3(SPRED1):c.46C>T (p.Arg16Ter)	SPRED1 (R16*)	Single nucleotide variant (nonsense)	Legius syndrome +2 more	GPathogenic
Select item 2189483	NM_152594.3(SPRED1):c.47G>T (p.Arg16Leu)	SPRED1 (R16L)	Single nucleotide variant (missense variant)	Legius syndrome	GUncertain significance
Select item 981594	NM_152594.3(SPRED1):c.47G>A (p.Arg16Gln)	SPRED1 (R16Q)	Single nucleotide variant (missense variant)	not provided +2 more	GUncertain significance
Select item 1308064	NM_152594.3(SPRED1):c.49G>C (p.Val17Leu)	SPRED1 (V17L)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 954199	NM_152594.3(SPRED1):c.49G>A (p.Val17Met)	SPRED1 (V17M)	Single nucleotide variant (missense variant)	Legius syndrome	GUncertain significance
Select item 1675562	NM_152594.3(SPRED1):c.50T>C (p.Val17Ala)	SPRED1 (V17A)	Single nucleotide variant (missense variant)	Legius syndrome +1 more	GUncertain significance
Select item 220213	NM_152594.3(SPRED1):c.51G>A (p.Val17=)	SPRED1	Single nucleotide variant (synonymous variant)	Legius syndrome	GLikely benign
Select item 2146310	NM_152594.3(SPRED1):c.52C>A (p.Arg18=)	SPRED1	Single nucleotide variant (synonymous variant)	Legius syndrome	GLikely benign
Select item 536693	NM_152594.3(SPRED1):c.52C>T (p.Arg18Ter)	SPRED1 (R18*)	Single nucleotide variant (nonsense)	Legius syndrome +1 more	GPathogenic
Select item 2737958	NM_152594.3(SPRED1):c.53G>T (p.Arg18Leu)	SPRED1 (R18L)	Single nucleotide variant (missense variant)	Legius syndrome	GUncertain significance
Select item 1400358	NM_152594.3(SPRED1):c.56C>G (p.Ala19Gly)	SPRED1 (A19G)	Single nucleotide variant (missense variant)	Legius syndrome	GUncertain significance
Select item 1375503	NM_152594.3(SPRED1):c.58G>C (p.Val20Leu)	SPRED1 (V20L)	Single nucleotide variant (missense variant)	Legius syndrome	GUncertain significance
Select item 2141687	NM_152594.3(SPRED1):c.60G>A (p.Val20=)	SPRED1	Single nucleotide variant (synonymous variant)	Legius syndrome	GLikely benign
Select item 1329066	NM_152594.3(SPRED1):c.60G>C (p.Val20=)	SPRED1	Single nucleotide variant (synonymous variant)	Cardiovascular phenotype +2 more	GLikely benign
Select item 546459	NM_152594.3(SPRED1):c.66G>T (p.Met22Ile)	SPRED1 (M22I)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 2202336	NM_152594.3(SPRED1):c.69C>T (p.Thr23=)	SPRED1	Single nucleotide variant (synonymous variant)	Legius syndrome +1 more	GLikely benign
Select item 1810	NM_152594.3(SPRED1):c.70C>T (p.Arg24Ter)	SPRED1 (R24*)	Single nucleotide variant (nonsense)	not provided +1 more	GPathogenic
Select item 1314093	NM_152594.3(SPRED1):c.71_72delinsTT (p.Arg24Leu)	SPRED1 (R24L)	Indel (missense variant)	not provided	GUncertain significance
Select item 373025	NM_152594.3(SPRED1):c.71G>A (p.Arg24Gln)	SPRED1 (R24Q)	Single nucleotide variant (missense variant)	Cardiovascular phenotype +1 more	GLikely pathogenic
Select item 391600	NM_152594.3(SPRED1):c.74A>G (p.Asp25Gly)	SPRED1 (D25G)	Single nucleotide variant (missense variant)	Legius syndrome +1 more	GUncertain significance
Select item 1334305	NM_152594.3(SPRED1):c.82A>G (p.Ser28Gly)	SPRED1 (S28G)	Single nucleotide variant (missense variant)	Legius syndrome +1 more	GUncertain significance
Select item 2891899	NM_152594.3(SPRED1):c.88G>A (p.Gly30Arg)	SPRED1 (G30R)	Single nucleotide variant (missense variant)	Legius syndrome	GUncertain significance
Select item 2714166	NM_152594.3(SPRED1):c.89G>T (p.Gly30Val)	SPRED1 (G30V)	Single nucleotide variant (missense variant)	Legius syndrome	GUncertain significance
Select item 1765780	NM_152594.3(SPRED1):c.90A>C (p.Gly30=)	SPRED1	Single nucleotide variant (synonymous variant)	Legius syndrome +1 more	GLikely benign

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