NM_015226.3:c.612C>A
Variant summary
Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2PP3
The NM_015226.3(CLEC16A):c.612C>A(p.Asn204Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000689 in 1,450,706 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015226.3 missense
Scores
Clinical Significance
Conservation
Publications
- schizophreniaInheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Uncertain_significance. The variant received 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLEC16A | ENST00000409790.6 | c.612C>A | p.Asn204Lys | missense_variant | Exon 7 of 24 | 5 | NM_015226.3 | ENSP00000387122.1 | ||
CLEC16A | ENST00000409552.4 | c.606C>A | p.Asn202Lys | missense_variant | Exon 6 of 21 | 1 | ENSP00000386495.3 | |||
CLEC16A | ENST00000703130.1 | c.606C>A | p.Asn202Lys | missense_variant | Exon 6 of 23 | ENSP00000515187.1 | ||||
CLEC16A | ENST00000494853.1 | n.87C>A | non_coding_transcript_exon_variant | Exon 2 of 8 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000673 AC: 1AN: 148588Hom.: 0 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.0000125 AC: 3AN: 239688 AF XY: 0.0000154 show subpopulations
GnomAD4 exome AF: 0.00000689 AC: 10AN: 1450706Hom.: 0 Cov.: 32 AF XY: 0.00000277 AC XY: 2AN XY: 721128 show subpopulations
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000673 AC: 1AN: 148588Hom.: 0 Cov.: 31 AF XY: 0.0000139 AC XY: 1AN XY: 72104 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.612C>A (p.N204K) alteration is located in exon 7 (coding exon 7) of the CLEC16A gene. This alteration results from a C to A substitution at nucleotide position 612, causing the asparagine (N) at amino acid position 204 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at