LOVD - Legend for PORCN



Sequence variations are described basically as recommended by the Ad-Hoc Nomenclature Committee of the Human Genome Variation Society (HGVS). For the most recent recommendations see the HGVS "Nomenclature for the description of sequence variants" web page. The most recent publication on the subject is by den Dunnen JT & Antonarakis SE (2000), Hum.Mut. 15: 7-12.

Genomic Reference Sequence.

NOTE: in all cases, unless indicated otherwise, all data of an entry are as reported by the author(s)/submitter.

Path.: Variant pathogenicity, in the format Reported/Concluded; '+' indicating the variant is pathogenic, '+?' probably pathogenic, '-' no known pathogenicity, '-?' probably no pathogenicity, '?' effect unknown.

Exon: Exon numbering.

DNA change: Variation at DNA level.

RNA change: Effect of change on RNA.
  • = = RNA change identical to DNA change
  • ? = unknown
  • (=) = no significant effect expected (but no experimental proof)
  • (0) = change expected to abolish transcription
  • (ex4ex5del) = probably deletion of exons 4 to 5
  • (ex4ex5dup) = probably duplication of exons 4 to 5
  • +cry = activation of cryptic splice site (no sequence published)
  • spl? = effect on splicing very likely (no experimental proof), examples;
    • splice donor site change (nucleotides +1 to +5 affected)
    • splice acceptor site change (nucleotides -2 to -1 affected)
    • new intronic AG splice acceptor di-nucleotide created close to (within 15 nucleotides) of normal splice acceptor site
  • (spl?) = might affect splicing (no experimental proof), examples;
    • change affects first or last nucleotide of exon
    • change creates strong splice donor or splice acceptor site in exon


Protein: Predicted effect of change on protein (usually without experimental proof!)
  • ? = unknown
  • (0) = change expected to abolish translation
  • ?fs = frame shift, but observed phenotype does not fit with prediction (for instance less severe phenotype (BMD) observed, more severe phenotype (DMD) expected)
  • ?no fs = frame shift, but observed phenotype does not fit with prediction (for instance more severe phenotype (DMD) observed, less severe phenotype (BMD) expected)
  • del = causes deletion
  • fs = causes frame shift
  • fs? = effect on reading frame very likely (no experimental proof)
  • (fs?) = might affect the reading frame (no experimental proof)
  • no fs = does not cause frame shift
  • X = stop codon (nonsense)


Variant Original description: Description as reported in the original article

Type: Type of variant at DNA level.
  • Substitution
  • Deletion
  • Duplication
  • Insertion
  • Inversion
  • Insertion/Deletion
  • Translocation
  • Other/Complex

Variant remarks: Variant remarks

PORCN DB-ID: Database IDentifier; When available, links to OMIM ID's are provided.

Origin: Variant origin = origin of variant allele, e.g. sporadic (no affected relatives besides brother/sister), de novo, familial (other affecteds besides brother/sister), consanguineous parents, etc.
  • ? (unknown)
  • in vitro (cloned)
  • familial
  • sporadic
  • sporadic, consanguineous parents
  • sporadic, non-consanguineous parents
  • sporadic, consanguinity parents?
  • de novo
  • de novo, somatic mosaicism
  • de novo, germline mosaicism
  • de novo, germline and somatic mosaicism
  • de novo, in patient
  • de novo, in patient (maternal allele)
  • de novo, in patient (paternal allele)
  • de novo, in mother
  • de novo, in mother (grandmaternal allele)
  • de novo, in mother (grandpaternal allele)
  • de novo, in father
  • de novo, in father (grandmaternal allele)
  • de novo, in father (grandpaternal allele)

X_inactivation: X skewing

Reference: Reference = report describing variant, incl. links to OMIM and dbSNP (when available); format {PMID[1]:[2]} (where [1] = PubMedID, [2] = e.g. den Dunnen 2007) or "den Dunnen ASHG2003 P2346"

Detection/Template: Template = template(s) used to detect the sequence variant; DNA = genomic DNA, RNA = RNA (cDNA), RNA+DNA = select both DNA and RNA
  • DNA = DNA
  • RNA = RNA (cDNA)
  • protein = protein
  • ? = unknown

Detection/Technique: Technique = technique(s) used to identify the sequence variants; select multiple when more were used
  • ? = unknown
  • arrayCGH = array for Comparative Genomic Hybridisation
  • arraySEQ = array for resequencing
  • arraySNP = array for SNP typing
  • arrayCNV = array for Copy Number Variation (SNP and CNV probes)
  • BESS = Base Excision Sequence Scanning
  • CMC = Chemical Mismatch Cleavage
  • CSCE = Conformation Sensitive Capillary Electrophoresis
  • ddF = dideoxy Fingerprinting
  • DGGE = Denaturing-Gradient Gel-Electrophoresis
  • DHPLC = Denaturing High-Performance Liquid Chromatography
  • DOVAM = Detection Of Virtually All Mutations (SSCA variant)
  • DSCA = Double-Strand DNA Conformation Analysis
  • EMC = Enzymatic Mismatch Cleavage
  • HD = HeteroDuplex analysis
  • IHC = Immuno-Histo-Chemistry
  • mPCR = multiplex PCR
  • MAPH = Multiplex Amplifiable Probe Hybridisation
  • MCA = high-resolution Melting Curve Analysis (hrMCA)
  • MLPA = Multiplex Ligation-dependent Probe Amplification
  • Northern = Northern blotting
  • PAGE = Poly-Acrylamide Gel-Electrophoresis
  • PCR = Polymerase Chain Reaction
  • PCRdig = PCR + restriction enzyme digestion
  • PFGE = Pulsed-Field Gel-Electrophoresis (+Southern)
  • PTT = Protein Truncation Test
  • RT-PCR = Reverse Transcription and PCR
  • SBE = Single Base Extension
  • SEQ = SEQuencing
  • Southern = Southern blotting
  • SSCA = Single-Strand DNA Conformation polymorphism Analysis (SSCP)
  • SSCAf = fluorescent SSCA (SSCP)
  • TaqMan = TaqMan assay
  • Western = Western Blotting

Disease: Disease phenotype of the patient(s).
  • FDH = FOCAL DERMAL HYPOPLASIA

Reference: Literature reference with possible link to publication in PubMed, dbSNP entry or other online resource. "Submitted:" indicates that the mutation was submitted directly to this database by the laboratory indicated.

Patient ID: Reference to the patient, such as a publication patient id.

Gender: Patient gender
  • Female
  • Male

Phenotype _Skin: Presence of major skin abnormalities: Skin hypoplasia; Hyperpigmentation; Fat herniation Nail dysplasia; Patchy alopecia; Papilloma periorally; Papilloma elsewhere (Yes, No, ND = non documented)
  • Patchy alopecia, Yes
  • Patchy alopecia, No
  • Patchy alopecia, ND
  • Nail dysplasia, Yes
  • Nail dysplasia, No
  • Nail dysplasia, ND
  • Skin hypoplasia, Yes
  • Skin hypoplasia, No
  • Skin hypoplasia, ND
  • Hyperpigmentation, Yes
  • Hyperpigmentation, No
  • Hyperpigmentation, ND
  • Fat herniation , Yes
  • Fat herniation , No
  • Fat herniation , ND
  • Papilloma periorally, Yes
  • Papilloma periorally, No
  • Papilloma periorally, ND
  • Papilloma elsewhere, Yes
  • Papilloma elsewhere, No
  • Papilloma elsewhere, ND

Phenotype_Skeleton: Presence of major Skeleton features: Oligodactily; Polydactily; Syndactily; Scoliosis; Other asymmetric limb defects (Yes, No, ND = not documented)
  • Syndactyly, Yes
  • Syndactyly, No
  • Syndactyly, ND
  • Scoliosis, Yes
  • Scoliosis, No
  • Scoliosis, ND
  • Polydactyly, Yes
  • Polydactyly, No
  • Polydactyly, ND
  • Asymmetrical skeletal defects, Yes
  • Asymmetrical skeletal defects, No
  • Asymmetrical skeletal defects, ND
  • Ectrodactyly, Yes
  • Ectrodactyly, No
  • Ectrodactyly, ND
  • Oligodactyly, Yes
  • Oligodactyly, No
  • Oligodactyly, ND

Phenotype_Oral_findings: Presence of major Oral findings features: Cleft lip/palate; Oligodontia; Enamel hypoplasia (Yes, No, ND = not documented)
  • Oligodontia, Yes
  • Oligodontia, No
  • Oligodontia, ND
  • Enamel hypoplasia, Yes
  • Enamel hypoplasia, No
  • Enamel hypoplasia, ND
  • Cleft lip/palate,Yes
  • Cleft lip/palate, No
  • Cleft lip/palate, ND

Thin_protruding_ears: Presence of thin, protruding ears (Yes, No, ND = not documented)
  • ND = non documented
  • Yes
  • No

Phenotype _Eye: Presence of major eye features: Significantly decreased vision, Microophtalmia, Coloboma, Tear duct obstruction (ND = not documented)
  • Significantly decreased vision, Yes
  • Significantly decreased vision , No
  • Significantly decreased vision , ND
  • Microophtalmia, Yes
  • Microophtalmia, No
  • Microophtalmia, ND
  • Coloboma, Yes
  • Coloboma, No
  • Coloboma, ND
  • Tear duct obstruction, Yes
  • Tear duct obstruction, No
  • Tear duct obstruction, ND

Microcephaly: Presence of major brain feature: Microcephaly Yes, No, ND (= not documented)
  • ND = not documented
  • Yes
  • No

Phenotype_Internal_organs: Presence of major internal organs features: Heart defects; Kidney malformation; Hydronephrosis; Displaced anus (Yes, No, ND = not documented)
  • Kidney malformation, Yes
  • Kidney malformation, No
  • Kidney malformation, ND
  • Hydronephrosis, Yes
  • Hydronephrosis, No
  • Hydronephrosis, ND
  • Heart defects , Yes
  • Heart defects , No
  • Heart defects, ND
  • Displaced anus, Yes
  • Displaced anus, No
  • Displaced anus, ND

Mental retardation: Presence of Mental Retardation: Yes, No, ND (= not documented)
  • ND = non documented
  • Yes
  • No

Phenotype_Other_findings: Presence of major Other features: Height lt P3-P10; Occipitofrontal circumference lt P3-P10; Mammary hypoplasia in adults; Nipple hypoplasia in adults; Hypohidrosis; Acral abnormalities; Caudal appendage; Omphalocele; Osteopathia striata (Striation of bones); IUGR (Intra Uterine Growth Retardation) (Yes, No, ND = not documented; lt = less than)
  • Osteopathia striata, Yes
  • Osteopathia striata, No
  • Osteopathia striata, ND
  • Omphalocele, Yes
  • Omphalocele, No
  • Omphalocele, ND
  • Occipitofrontal circumference lt P3-P10, Yes
  • Occipitofrontal circumference lt P3-P10, No
  • Occipitofrontal circumference lt P3-P10, ND
  • Nipple hypoplasia in adults, Yes
  • Nipple hypoplasia in adults, No
  • Nipple hypoplasia in adults, ND
  • Mammary hypoplasia in adults, Yes
  • Mammary hypoplasia in adults, No
  • Mammary hypoplasia in adults, ND
  • Hypohidrosis, Yes
  • Hypohidrosis, No
  • Hypohidrosis, ND
  • Height lt P3-P10, Yes
  • Height lt P3-P10, No
  • Height lt P3-P10, ND
  • Caudal appendage, Yes
  • Caudal appendage, No
  • Caudal appendage, ND
  • Acral abnormalities, Yes
  • Acra abnormalities, No
  • Acral abnormalities, ND
  • IUGR, Yes
  • IUGR, No
  • IUGR, ND

Phenotype additional: Phenotype, additional features

# Reported: Number of times this case has been reported

Geographic origin: Geographic origin of the patient

Ethnic origin: Ethnic origin of the patient