SPRED1 Database

  • Reference sequences were NC_000015.9 and NM_152594.2. cDNA number 1 is the "A" of the start codon.
  • Frameshift is documented by the original amino acid followed by the codon number and "fs" (ex. Leu159 fs).
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Click for a detailed description of: NIH Diagnostic Criteria for NF1

99 variants found

Genomic Position Location Mutation Type Nucleotide Change Protein Change Classification Legius Syndrome Phenotype References Comments
38545386 Promoter-Exon 1 Large deletion c.1-?_c.32+? p.0 Pathogenic Multiple CALMs, mild learning disabilities; found in father who had multiple CALMs. Spencer (2011)
38545386 Promoter-Exon 4 Large deletion c.1-1175-?_423+19+?del p.? Pathogenic Brems (2012)  
38545387 Exon 1-7 Large deletion c.1-?_c.1335+? p.0 Pathogenic Multiple CALMs and axillary freckling. Spencer (2011)
38545388 Exon 1-7 Large deletion c.1-?_c.1335+? p.0 Pathogenic Multiple CALMs, speech delay and mild developmental delay. Spencer (2011)
38545390 Exon 1 Missense c.2T>C p.Met1? Uncertain Multiple CALMs, axillary and inguinal freckling, cephalalgia, learning disability, ADHD and developmental delay. Pasmant (2009)
38545393 Exon 1 Nonsense c.7G>T p.Glu3X Pathogenic Multiple CALMs and hyperactivity. Messiaen (2009)
38545393 Exon 1 Deletion c.7_20del p.Glu3PhefsX2 Pathogenic Multiple CALMs, axillary and inguinal freckling, head circumference in the 10-25th percentile. Messiaen (2009)
38545412 Exon 1 Missense c.26A>T p.Asp9Val Uncertain Not given. Brems (2012)
38545416 Exon 1 Missense c.30C>A p.Asn10Lys Uncertain Not given. Brems (2012)  
38591574 Exon 2-6 In/del c.33-20604_684+401
delinsGAAA		 p.? Pathogenic Multiple CALMs, bilateral axillary and inguinal freckling, ADHD and lipomas. Spencer (2011)
38591583 Exon 1 Silent c.42T>C p.= Benign Multiple CALMs, other small pigmented spots and axillary freckling. Messiaen (2009)
38591587 Exon 2 Nonsense c.46C>T p.Arg16X Pathogenic Multiple CALMs and learning disability (Pasmant). Multiple CALMs and punctate freckling in groin (Spurlock). Pasmant (2009)
38591593 Exon 2 Nonsense c.52C>T p.Arg18X Pathogenic Multiple CALMs, thoracic freckling, head circumference in the 75-90th percentile, speech delay with normal intelligence, meatal stenosis, hypertelorism, mild hearing loss in left ear (Messiaen). Multiple CALMs, axillary and inguinal freckling, learning di Messiaen (2009)
38591601 Exon 2 Insertion c.60_61insC p.Val21ArgfsX6 Pathogenic Multile CALMs, head circumference in the 50-75th percentile and hyperactivity. Messiaen (2009)
38591611 Exon 2 Nonsense c.70C>T p.Arg24X Pathogenic Multiple CALMs, mild to no freckling, head circumference percentile ranged from 3-97, lipomas, developmental delay and ADHD as well as one family member with cataract and another with eczema (Brems). Multiple CALMs, no other NF1 diagnostic signs (Spencer) Brems (2007)
38591612 Exon 2 Missense c.71G>A p.Arg24Gln Uncertain Multiple CALMs, no other NF1 diagnostic signs. Spencer (2011)
38591628 Exon 2 Duplication c.87_88dupTG p.Gly30ValfsX11 Pathogenic Multiple CALMs, no other NF1 diagnostic signs. Spencer (2011)  
38591629 Exon 2 Missense c.88G>A p.Gly30Arg Uncertain Multiple CALMs, no other NF1 diagnostic signs. Spencer (2011)
38591634 Exon 2 Missense c.93G>T p.Trp31Cys Pathogenic Multiple CALMs, axillary freckling, developmental delay and ADHD. Denayer (2010)
38591665 Exon 2 Missense c.124G>A p.Val42Ile Uncertain Multiple CALMs, no other NF1 diagnostic signs. Spencer (2011)
38591672 Exon 2 Missense c.131T>A p.Val44Asp Suspected Pathogenic Multiple CALMs, freckling and head circumference ranging from normal to 98th percentile. Spurlock (2009)  
38591689 Exon 2 Nonsense c.148C>T p.Gln50X Pathogenic Brems (2012)  
38591725 Exon 2 Missense c.184G>C p.Gly62Arg Pathogenic Multiple CALMs. Sumner et al, unpublished
38591731 Exon 2 Nonsense c.190C>T p.Arg64X Pathogenic Multiple CALMs (Brems). Mutation tracked with disease, multiple CALMs, macrocephaly, axillary and inguinal freckling, lipoma, learning disability and cephalalgia (Pasmant). Multiple CALMs, bilateral axillary freckling, head circumferences ranged from the Brems (2007)
38591785 Intron 2 Intronic c.207+37A>G p.? Benign Assumed benign. dbSNP
38614451 Exon 3 Nonsense c.217G>T p.Glu73X Pathogenic Multiple CALMs, head circumference in the 9th and 9oth percentile. Spurlock (2009)
38614454 Exon 3 Missense c.221G>T p.Cys74Phe Suspected Benign Multiple CALMs, freckling only in hyperpigmented quadrant, segmental pigmentary NF phenotype. Messiaen (2009)
38614473 Exon 3 Missense c.239T>G p.Leu80Arg Uncertain Multiple CALMs. Spencer (2011)
38614476 Exon 3 Deletion c.242_256del p.Ile81_Val85del Pathogenic Multiple CALMs (Brems). Multiple CALMs, some axillary and inguinal pigmentation, head circumference in the 60th percentile, normal brain MRI and pectus excavatum (Messiaen 2009). Brems (2007)
38614503 Exon 3 Deletion c.269delA p.His90ProfsX31 Pathogenic Brems (2012)  
38614505 Exon 3 Deletion c.271delC p.His91ThrfsX30 Pathogenic Multiple CALMs. Messiaen (2009)
38614525 Exon 3 Silent c.291G>A p.= Benign Muram-Zborovski (2010)
38614533 Exon 3 Missense c.299G>A p.Gly100Asp Uncertain Not given. Brems (2012)  
38614538 Exon 3 Duplication c.304dupA p.Thr102AsnfsX7 Pathogenic Multiple CALMs (Brems). Multiple CALMs and learning difficulties (Denayer). Brems (2007)
38614539 Exon 3 Deletion c.305delC p.Thr102SerfsX19 Pathogenic Multiple CALMs. Spencer (2011)  
38614539 Exon 3 Missense c.305C>G p.Thr102Arg Pathogenic Multiple CALMs, some axilary and inguinal freckling, head circumferences ranging from the 25-75th percentile. Messiaen (2009)
38614540 Exon 3 Missense c.305C>A p.Thr102Lys Uncertain Multiple CALMs. Spencer (2011)
38614541 Exon 3 Missense c.305C>T p.Thr102Met Uncertain Multiple CALMs. Spencer (2011)
38614554 Exon 3 Deletion c.320_333del p.Ala107Valfsx2 Pathogenic Multiple CALMs, axillary/inguinal freckling and head circumferences ranging from 50th to greater than the 97th percentile. Messiaen (2009)
38614560 Exon 3 Duplication c.326_329dupCTAG p.Ala110SerfsX2 Pathogenic Multiple CALMs (Messiaen). Multiple CALMs, axillary freckling, ADHD (Denayer 2010). Messiaen (2009)
38614583 Exon 3 Nonsense c.349C>T p.Arg117X Pathogenic Multiple CALMs, lipomas, and head circumference percentile ranging from 25-97. Multiple CALMs and developmental delay (Denayer). Brems (2007)
38614594 Exon 3 Insertion c.360dupA p.Glu121ArgfsX13 Pathogenic Multiple CALMs and learning disability. Denayer (2010)
38616962 Intron 3 Splice Site c.377-2A>C p.Cys127LysfsX2 Pathogenic Brems (2012)
38617004 Exon 4 Silent c.417C>T p.= Benign dbSNP
38617011 Intron 4 Splice Site c.423+1G>A p.Cys127LysfsX2 Uncertain Multiple CALMs, varying degrees of freckling, head circumference percentile ranged from 50-97 and learning difficulty. Brems (2007)
38631920 Intron 4 Intronic c.424-18G>A p.? Benign dbSNP
38631930 Intron 4 Intronic c.424-8C>A p.? Benign Muram-Zborovski (2010)
38631960 Exon 5 Missense c.446G>A p.Ser149Asn Suspected Benign Multiple CALMs (Brems and Messiaen). Brems (2007)
38631974 Exon 5 Duplication c.460_463dupGATC p.His155ArgfsX13 Pathogenic Brems (2012)  
38631982 Exon 5 Insertion c.468_469insGA p.Phe157AspfsX18 Pathogenic Multiple CALMs. Spencer (2011)  
38631983 Exon 5 Insertion c.468_469insCA p.Phe157fs Pathogenic Multiple CALMs. Messiaen (2009)
38631989 Exon 5 Nonsense c.475C>T p.Gln159X Pathogenic Brems (2012)  
38632007 Exon 5 Deletion c.493delA p.Ser165ValfsX9 Pathogenic Multiple CALMs. Spencer (2011)  
38632078 Exon 5 Missense c.564G>A p.Met188Ile Suspected Benign Multiple CALMs. Messiaen (2009)
38632090 Exon 5 Duplication c.576_580dupCAATC p.Gln194ProfsX4 Pathogenic Multiple CALMs, axillary freckling and mild learning disability. Denayer (2010)
38632094 Exon 5 Nonsense c.580C>T p.Gln194X Pathogenic Multiple CALMs, axillary and inguinal freckling, learning disabilities and head circumference: greater than 98th percentile. Muram-Zborovski (2010)
38641627 Exon 6 Missense c.587C>T p.Thr196Ile Suspected Benign Multiple CALMs (Spencer). Multiple CALMs and abnormal development (Messiaen). Messiaen (2009)
38641645 Exon 6 Nonsense c.605T>A p.Leu202X Pathogenic Multiple CALMs. Messiaen (2009)
38641674 Exon 6 Missense c.634G>A p.Val212Ile Uncertain Multiple CALMs. Spencer (2011)
38641677 Exon 6 Nonsense c.637C>T p.Gln213X Pathogenic Multiple CALMs, axillary and inguinal freckling and learning disability. Pasmant (2009)
38641683 Exon 6 Nonsense c.643C>T p.Gln215X Pathogenic Multiple CALMs and lipomas. Brems (2007)
38641707 Exon 6 Deletion c.667delC p.Leu223X Pathogenic Multiple CALMs. Spencer (2011)  
38641773 Intron 6 Intronic c.684+49_684+50
insTTAAATT		 p.? Benign dbSNP
38643230 Exon 7 Duplication c.700dupA p.Ile234AsnfsX9 Pathogenic Not given Leiden Database (LOVD)  
38643230 Exon 7 Deletion c.700_703del p.Ile234AspfsX14 Pathogenic Multiple CALMs and head circumference: greater than 95th percentile. Messiaen (2009)
38643297 Exon 7 Missense c.767G>A p.Arg256His Uncertain Five month old with CALMs and hypopigmentation (database submission). Brems (2012)
38643299 Exon 7 Missense c.769C>T p.Arg257Cys Uncertain Brems (2012)
38643311 Exon 7 Deletion c.781del p.? Pathogenic Multiple CALMs and Crowe sign. Lopez (2011)
38643314 Exon 7 Nonsense c.784A>T p.Arg262X Pathogenic Multiple CALMs, axillary and inguinal freckling. Spurlock (2009)
38643326 Exon 7 Deletion c.796_797delAT p.Met266ValfsX4 Pathogenic Multiple CALMs. Brems (2007)
38643351 Exon 7 Missense c.821A>G p.Asp274Gly Suspected Benign Brems (2012)
38643362 Exon 7 Duplication c.832dupT p.Ser278PhefsX7 Pathogenic Brems (2012)  
38643453 Exon 7 Deletion c.923_924delCT p.Ser308CysfsX4 Pathogenic Multiple CALMs, head circumference: 25-50th and 97th percentile. Messiaen (2009)
38643456 Exon 7 Missense c.926T>C p.Val309Ala Uncertain Multiple CALMs. Spencer (2011)
38643468 Exon 7 Missense c.938C>T p.Thr313Met Suspected Benign Multiple CALMs. Messiaen (2009)
38643470 Exon 7 Nonsense c.940C>T p.Gln314X Pathogenic Multiple CALMs, axillary and inguinal freckling, macrocephaly and mild learning disability. Denayer (2010)
38643474 Exon 7 Missense c.944C>T p.Pro315Leu Suspected Benign Brems (2012)
38643494 Exon 7 Nonsense c.964A>T p.Lys322X Pathogenic Multiple CALMs, head circumferences: greater than 97th, 97th and 90-97th percentile (Messiaen 2009). Brems (2007)
38643503 Exon 7 Nonsense c.973C>T p.Arg325X Pathogenic Multiple CALMs and family history or CALMS (Brems). Multiple CALMs, axillary and inguinal freckling, head circumferences: 10th, 25-50th percentile, abnormal development: special education and ADHD and language delay (Messian). Brems (2007)
38643519 Exon 7 Deletion c.989delG p.Gly330ValfsX76 Pathogenic Brems (2012)  
38643521 Exon 7 Nonsense c.991G>T p.Glu331X Pathogenic Multiple CALMs. Spencer (2011)  
38643561 Exon 7 Missense c.1031A>G p.His344Arg Uncertain Multiple CALMs. Spencer (2011)
38643574 Exon 7 Silent c.1044T>C p.Val348Val Benign Muram-Zborovski (2010)
38643575 Exon 7 Deletion c.1045_1046delAG p.Arg349GlyfsX11 Pathogenic Multiple CALMs, general and inguinal freckling, macrocephaly, suspected autism. Denayer (2010)
38643577 Exon 7 Deletion c.1048_1049delGG p.Gly350LysfsX10 Pathogenic Multiple CALMs and freckling. Spurlock (2009)
38643578 Exon 7 Deletion c.1048_1060del p.Gly350MetfsX52 Pathogenic Multiple CALMs, diffuse freckling (Pasamant). Multiple CALMs, macrocephaly, ADHD and lipomas (Denayer). Pasmant (2009)
38643579 Exon 7 Deletion c.1149_1152delAGAG p.Gly350AspfsX55 Pathogenic Multiple CALMs (Brems). Multiple CALMs without freckling (Spurlock). Multiple CALMs, axillary and inguinal freckling, head circumferences: 90-97th and 50th percentile; also found, angiolipoma (Messiaen). Multiple CALMs, axillary and inguinal freckling (De Brems (2007)
38643609 Exon 7 Deletion c.1073delC p.Pro358LeufsX48 Pathogenic Multiple CALMs. Spencer (2011)  
38643722 Exon 7 Missense c.1192G>A p.Asp398Asn Suspected Benign Multiple CALMs (Spencer 2011). Multiple CALMs and hyperactivity (Messiaen). Messiaen (2009)
38643734 Exon 7 Duplication c.1204_1207dupTTGC p.Arg403LeufsX30 Pathogenic Multiple CALMs and head circumference 90th percentile. Messiaen (2009)
38643753 Exon 7 Missense c.1223T>A p.Val408Glu Uncertain Brems (2012)
38643773 Exon 7 Missense c.1243C>G p.Pro415Ala Pathogenic Multiple CALMs, axillary pigmentation, head circumferences: 20th and 75th percentile, language delay and fine motor delay. Messiaen (2009)
38643776 Exon 7 Missense c.1246C>T p.Cys416Arg Uncertain Multiple CALMs. Spencer (2011)
38643778 Exon 7 Duplication c.1248dupT p.Met417TyrfsX15 Suspected Pathogenic Multiple CALMs and inguinal freckling. Messiaen (2009)
38643782 Exon 7 Deletion c.1252delT p.Cys418AlafsX6 Pathogenic Multiple CALMs (Spencer). Multiple CALMs, axillary and inguinal freckling, head circumferences: much greater than 97th and 90-95th percentile, language delay and developmental delay, seizures and one patient with unequal gluteal folds (Messiaen). Messiaen (2009)
38643803 Exon 7 Missense c.1273A>G p.Met425Val Uncertain Brems (2012)
38643819 Exon 7 Missense c.1289G>C p.Gly430Ala Uncertain Brems (2012)  
38643819 Exon 7 Deletion c.1289_1298del p.Gly430ValfsX29 Pathogenic Brems (2012)
38643828 Exon 7 Missense c.1298G>A p.Cys433Tyr Suspected Benign Messiaen (2009)