13-24321070-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_178540.5(C1QTNF9):c.304C>T(p.Pro102Ser) variant causes a missense change. 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 Uncertain significance (★).
Frequency
Consequence
NM_178540.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C1QTNF9 | NM_178540.5 | c.304C>T | p.Pro102Ser | missense_variant | Exon 4 of 4 | ENST00000332018.5 | NP_848635.2 | |
C1QTNF9 | NM_001303137.2 | c.304C>T | p.Pro102Ser | missense_variant | Exon 5 of 5 | NP_001290066.1 | ||
C1QTNF9 | NM_001303138.2 | c.304C>T | p.Pro102Ser | missense_variant | Exon 4 of 4 | NP_001290067.1 | ||
PCOTHP1 | n.24321070C>T | intragenic_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C1QTNF9 | ENST00000332018.5 | c.304C>T | p.Pro102Ser | missense_variant | Exon 4 of 4 | 1 | NM_178540.5 | ENSP00000333737.4 | ||
C1QTNF9 | ENST00000382071.6 | c.304C>T | p.Pro102Ser | missense_variant | Exon 4 of 4 | 5 | ENSP00000371503.2 | |||
C1QTNF9-AS1 | ENST00000449656.1 | n.73+456G>A | intron_variant | Intron 1 of 1 | 5 | |||||
ENSG00000273167 | ENST00000382141.4 | n.*300C>T | downstream_gene_variant | 5 | ENSP00000371576.4 |
Frequencies
GnomAD3 genomes Cov.: 21
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 7.54e-7 AC: 1AN: 1325926Hom.: 0 Cov.: 27 AF XY: 0.00000151 AC XY: 1AN XY: 661716
GnomAD4 genome Cov.: 21
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.304C>T (p.P102S) alteration is located in exon 4 (coding exon 3) of the C1QTNF9 gene. This alteration results from a C to T substitution at nucleotide position 304, causing the proline (P) at amino acid position 102 to be replaced by a serine (S). 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
Publications
No publications associated with this variant yet.