chr13-95552897-C-G
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PM5PP3_ModeratePP5
The NM_006984.5(CLDN10):āc.144C>Gā(p.Asn48Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,844 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 Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N48H) has been classified as Likely pathogenic.
Frequency
Consequence
NM_006984.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLDN10 | NM_006984.5 | c.144C>G | p.Asn48Lys | missense_variant | 1/5 | ENST00000299339.3 | |
CLDN10 | XM_047430765.1 | c.-3108C>G | 5_prime_UTR_variant | 1/6 | |||
CLDN10 | NM_001160100.2 | c.158-7235C>G | intron_variant | ||||
CLDN10 | NM_182848.4 | c.215-7235C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLDN10 | ENST00000299339.3 | c.144C>G | p.Asn48Lys | missense_variant | 1/5 | 1 | NM_006984.5 | P1 | |
CLDN10 | ENST00000376873.7 | c.215-7235C>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461844Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727234
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
HELIX syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 15, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at