3-190402428-C-T
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PP3_StrongPP5_Moderate
The NM_006580.4(CLDN16):c.206C>T(p.Ala69Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000868 in 1,612,272 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 Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. A69A) has been classified as Likely benign.
Frequency
Consequence
NM_006580.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLDN16 | NM_006580.4 | c.206C>T | p.Ala69Val | missense_variant | Exon 2 of 5 | ENST00000264734.3 | NP_006571.2 | |
CLDN16 | NM_001378492.1 | c.206C>T | p.Ala69Val | missense_variant | Exon 6 of 9 | NP_001365421.1 | ||
CLDN16 | NM_001378493.1 | c.206C>T | p.Ala69Val | missense_variant | Exon 5 of 8 | NP_001365422.1 | ||
CLDN16 | XM_047447333.1 | c.206C>T | p.Ala69Val | missense_variant | Exon 4 of 7 | XP_047303289.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLDN16 | ENST00000264734.3 | c.206C>T | p.Ala69Val | missense_variant | Exon 2 of 5 | 1 | NM_006580.4 | ENSP00000264734.3 | ||
CLDN16 | ENST00000456423.2 | c.115-7475C>T | intron_variant | Intron 1 of 1 | 1 | ENSP00000414136.2 | ||||
CLDN16 | ENST00000468220.1 | n.398C>T | non_coding_transcript_exon_variant | Exon 4 of 5 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151952Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251426Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135876
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1460320Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 726610
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151952Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74190
ClinVar
Submissions by phenotype
Primary hypomagnesemia Pathogenic:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at