chrX-106927928-G-GTTT
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_020384.4(CLDN2):c.-178-115_-178-113dupTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000941 in 85,032 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. There is a variant allele frequency bias in the population database for this variant (GnomAdExome4), which may indicate mosaicism or somatic mutations in the reference population data. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., 0 hem., cov: 0)
Exomes 𝑓: 0.000094 ( 0 hom. 0 hem. )
Failed GnomAD Quality Control
Consequence
CLDN2
NM_020384.4 intron
NM_020384.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.223
Publications
0 publications found
Genes affected
CLDN2 (HGNC:2041): (claudin 2) This gene product belongs to the claudin protein family whose members have been identified as major integral membrane proteins localized exclusively at tight junctions. Claudins are expressed in an organ-specific manner and regulate tissue-specific physiologic properties of tight junctions. This protein is expressed in the intestine. Alternatively spliced transcript variants with different 5' untranslated region have been found for this gene.[provided by RefSeq, Jan 2010]
MORC4 (HGNC:23485): (MORC family CW-type zinc finger 4) In human, the four current members of the microrchidia (morc) gene family share an N-terminal ATPase-like ATP-binding region and a CW four-cysteine zinc-finger motif. The protein encoded by this gene also has a nuclear matrix binding domain and a two-stranded coiled-coil motif near its C-terminus. This gene is widely expressed at low levels in normal tissues and has elevated expression in placenta and testis. Alternative splicing results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, Jan 2010]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_020384.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CLDN2 | NM_020384.4 | MANE Select | c.-178-115_-178-113dupTTT | intron | N/A | NP_065117.1 | P57739 | ||
| CLDN2 | NM_001171092.1 | c.-178-115_-178-113dupTTT | intron | N/A | NP_001164563.1 | P57739 | |||
| CLDN2 | NM_001171095.2 | c.-178-115_-178-113dupTTT | intron | N/A | NP_001164566.1 | P57739 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CLDN2 | ENST00000336803.2 | TSL:2 MANE Select | c.-178-123_-178-122insTTT | intron | N/A | ENSP00000336571.1 | P57739 | ||
| CLDN2 | ENST00000540876.1 | TSL:1 | c.-178-123_-178-122insTTT | intron | N/A | ENSP00000443230.1 | P57739 | ||
| CLDN2 | ENST00000541806.6 | TSL:1 | c.-178-123_-178-122insTTT | intron | N/A | ENSP00000441283.1 | P57739 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 107515Hom.: 0 Cov.: 0
GnomAD3 genomes
AF:
AC:
0
AN:
107515
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0000941 AC: 8AN: 85032Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 20492 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
8
AN:
85032
Hom.:
AF XY:
AC XY:
0
AN XY:
20492
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1
AN:
2156
American (AMR)
AF:
AC:
2
AN:
2913
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3022
East Asian (EAS)
AF:
AC:
1
AN:
4832
South Asian (SAS)
AF:
AC:
2
AN:
1081
European-Finnish (FIN)
AF:
AC:
0
AN:
6032
Middle Eastern (MID)
AF:
AC:
1
AN:
410
European-Non Finnish (NFE)
AF:
AC:
1
AN:
58746
Other (OTH)
AF:
AC:
0
AN:
5840
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.238
Heterozygous variant carriers
0
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0.20
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0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
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4
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Age
GnomAD4 genome 0.00 AC: 0AN: 107515Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 30417
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
107515
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
30417
African (AFR)
AF:
AC:
0
AN:
29532
American (AMR)
AF:
AC:
0
AN:
10080
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2595
East Asian (EAS)
AF:
AC:
0
AN:
3398
South Asian (SAS)
AF:
AC:
0
AN:
2476
European-Finnish (FIN)
AF:
AC:
0
AN:
5261
Middle Eastern (MID)
AF:
AC:
0
AN:
226
European-Non Finnish (NFE)
AF:
AC:
0
AN:
51846
Other (OTH)
AF:
AC:
0
AN:
1438
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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