Craniofacial anomalies
WNT5A (Wnt family member 5A)
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Unique variants in gene WNT5A
The variants shown are described using the NM_003392.4 transcript reference sequence.
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Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column's header and hold it still. Below, a more detailed description is shown per column.
Effect
: The variant's effect on the protein's function, in the format Reported/Curator concluded; '+' indicating the variant affects function, '+?' probably affects function, '+*' affects function, not associated with individual's disease phenotype, '#' affects function, not associated with any known disease phenotype, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect not classified.
Reported
: The number of times this variant has been reported in the database.
Exon
: Number of exon/intron containing variant; 2 = exon 2, 12i = intron 12, 2i_7i = exons 3 to 7, 8i_9 = border intron 8/exon 9.
DNA change (cDNA)
: Description of variant at DNA level, based on a coding DNA reference sequence (following HGVS recommendations); e.g. c.123C>T, c.123_145del, c.123_126dup.
Position
: Position of variant in coding DNA sequence; note that coding DNA position can also be derived from the variant description.
RNA change
: Description of variant at RNA level (following HGVS recommendations).
r.123c>u
r.? = unknown
r.(?) = RNA not analysed but probably transcribed copy of DNA variant
r.spl? = RNA not analysed but variant probably affects splicing
r.(spl?) = RNA not analysed but variant may affect splicing
r.0? = change expected to abolish transcription
Protein
: Description of variant at protein level (following HGVS recommendations).
p.(Arg345Pro) = change predicted from DNA (RNA not analysed)
p.Arg345Pro = change derived from RNA analysis
p.? = unknown effect
p.0? = probably no protein produced
PolyPhen prediction
: Effect of variant, predicted by PolyPhen.
All options:
benign = Benign
possiblyDamaging = Possibly damaging
probablyDamaging = Probably damaging
noPrediction = No prediction
Allele
: On which allele is the variant located? Does not necessarily imply inheritance! 'Paternal' (confirmed or inferred), 'Maternal' (confirmed or inferred), 'Parent #1' or #2 for compound heterozygosity without having screened the parents, 'Unknown' for heterozygosity without having screened the parents, 'Both' for homozygozity.
DNA change (genomic) (hg38)
: Description of variant at DNA level, based on the genomic DNA reference sequence (following HGVS recommendations).
g.12345678C>T
g.12345678_12345890del
g.12345678_12345890dup
Reference
: Reference to publication describing the variant, including links to OMIM (when available), PubMed or or other source, e.g. "den Dunnen ASHG2003 P2346".
DB-ID
: Database ID of variant, grouping multiple observations of the same variant together, starting with the HGNC gene symbol, followed by an underscore (_) and a six digit number (e.g. DMD_012345). _000000 is used for variants where DNA was not analysed (change predicted from RNA analysis), variants seen in animal models or variants not seen in humans but functionally tested in vitro.
Frequency
: Frequency in which the variant was found; e.g 5/760 chromosomes (in 5 of 760 chromosomes tested), 1/33 patients (in 1 of 33 patients analysed in study), 0.05 controls (in 5% of control cases tested).
Allele Count
: Allele count on genotypes, for each ALT allele. Meaning, if the allele is 0/1 the count is 1; if is 1/1 the count is 2; if is 0/0 the count is 0.
Allele Number
: Total number of alleles in called genotypes
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Effect
Reported
Exon
DNA change (cDNA)
Position
RNA change
Protein
PolyPhen prediction
DNA change (genomic) (hg38)
Reference
DB-ID
Frequency
Allele Count
Allele Number
Owner
./.
10
-
c.6+230A>C
-
r.(=)
p.(=)
-
g.55486750T>G
dbSNP
WNT5A_000007
0.732 Control, 0.500 Patients_Q37.0, 0.500 Patients_Q37.2, 0.500 Patients_Q37.3_left,
6 more items
521, 1, 2, 5, 74, 81, 28, 42
712, 2, 4, 6, 104, 116, 48, 58
Admin
./.
7
-
c.7-2017C>G
-
r.(=)
p.(=)
-
g.55482935G>C
dbSNP
WNT5A_000006
0.127 Control, 0.250 Patients_Q37.2, 0.167 Patients_Q37.3_right, 0.132 Patients_Q37.4,
3 more items
91, 1, 14, 10, 3
716, 4, 6, 106, 120, 48, 58
Admin
./.
10
-
c.391+1667C>T
-
r.(=)
p.(=)
-
g.55477647G>A
dbSNP
WNT5A_000005
0.469 Control, 0.500 Patients_Q37.0, 0.250 Patients_Q37.2, 0.250 Patients_Q37.3_left,
6 more items
333, 1, 3, 41, 40, 15, 30
710, 2, 4, 6, 104, 116, 46, 56
Admin
./.
8
-
c.685-812C>G
-
r.(=)
p.(=)
-
g.55471362G>C
dbSNP
WNT5A_000004
0.373 Control, 0.250 Patients_Q37.3_left, 0.167 Patients_Q37.3_right, 0.265 Patients_Q37.4,
4 more items
265, 1, 27, 36, 13, 24
710, 4, 6, 102, 118, 48, 56
Admin
./.
10
-
c.685-152T>C
-
r.(=)
p.(=)
-
g.55470702A>G
dbSNP
WNT5A_000003
0.534 Control, 0.500 Patients_Q37.0, 0.250 Patients_Q37.2, 0.250 Patients_Q37.3_left,
6 more items
379, 1, 4, 57, 58, 19, 36
710, 2, 4, 6, 106, 120, 48, 58
Admin
./.
8
-
c.*2945A>G
-
r.(=)
p.(=)
-
g.55467147T>C
dbSNP
WNT5A_000002
0.471 Control, 0.750 Patients_Q37.2, 0.750 Patients_Q37.3_left, 0.431 Patients_Q37.4,
4 more items
329, 3, 44, 1, 58, 23, 20
698, 4, 102, 2, 114, 46, 58
Admin
./.
9
-
c.*3712A>T
-
r.(=)
p.(=)
-
g.55466380T>A
dbSNP
WNT5A_000001
0.462 Control, 0.750 Patients_Q37.2, 0.750 Patients_Q37.3_left, 0.333 Patients_Q37.3_right,
5 more items
330, 3, 2, 52, 62, 28, 20
714, 4, 6, 106, 120, 48, 58
Admin
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