NM_017410.3:c.390C>A
Variant names:
Variant summary
Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_017410.3(HOXC13):c.390C>A(p.Tyr130*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
HOXC13
NM_017410.3 stop_gained
NM_017410.3 stop_gained
Scores
2
4
1
Clinical Significance
Conservation
PhyloP100: 0.627
Publications
2 publications found
Genes affected
HOXC13 (HGNC:5125): (homeobox C13) This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, which are located on different chromosomes and consist of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXC genes located in a cluster on chromosome 12. The product of this gene may play a role in the development of hair, nail, and filiform papilla. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 11 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 12-53939296-C-A is Pathogenic according to our data. Variant chr12-53939296-C-A is described in ClinVar as Pathogenic. ClinVar VariationId is 39781.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| HOXC13 | ENST00000243056.5 | c.390C>A | p.Tyr130* | stop_gained | Exon 1 of 2 | 1 | NM_017410.3 | ENSP00000243056.3 | ||
| HOXC13-AS | ENST00000512916.3 | n.222+175G>T | intron_variant | Intron 1 of 2 | 3 | |||||
| HOXC13-AS | ENST00000810609.1 | n.181+175G>T | intron_variant | Intron 1 of 2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1422206Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 704310
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1422206
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
704310
African (AFR)
AF:
AC:
0
AN:
32550
American (AMR)
AF:
AC:
0
AN:
39248
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25422
East Asian (EAS)
AF:
AC:
0
AN:
37412
South Asian (SAS)
AF:
AC:
0
AN:
81662
European-Finnish (FIN)
AF:
AC:
0
AN:
48064
Middle Eastern (MID)
AF:
AC:
0
AN:
5728
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1093276
Other (OTH)
AF:
AC:
0
AN:
58844
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Ectodermal dysplasia 9, hair/nail type Pathogenic:1
Nov 02, 2012
OMIM
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:literature only
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
PhyloP100
Vest4
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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