17-6624770-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP5BP4
The NM_001351225.2(KIAA0753):c.-425C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000263 in 1,406,662 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001351225.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000650 AC: 11AN: 169322Hom.: 0 AF XY: 0.0000778 AC XY: 7AN XY: 89940
GnomAD4 exome AF: 0.0000263 AC: 37AN: 1406662Hom.: 0 Cov.: 30 AF XY: 0.0000259 AC XY: 18AN XY: 694570
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Pathogenic:2Benign:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Clinical Genetics and Genomics, Karolinska University Hospital | Nov 20, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 10, 2022 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Mar 10, 2025 | RNA studies demonstrate a damaging effect as this variant leads to aberrant exon 4 skipping when present in the homozygous state (PMID: 33875766); Nucleotide is not conserved across species and the substitution has no predicted effect on splicing; This variant is associated with the following publications: (PMID: 29138412, 39806532, 33875766, 33726816) - |
Orofaciodigital syndrome XV;C5561958:Joubert syndrome 38;C5561961:Short-rib thoracic dysplasia 21 without polydactyly Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 03, 2024 | - - |
Short-rib thoracic dysplasia 21 without polydactyly Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 07, 2021 | - - |
Jeune thoracic dystrophy;C0431399:Familial aplasia of the vermis Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Rare Disease Group, Clinical Genetics, Karolinska Institutet | Jun 11, 2019 | This synonymous variant has been shown to affect splicing, leading to skipping of exon 4 in the KIAA0753 protein (shown by sequencing cDNA from homozygous individual). Four deceased patients (from two families) with SRTD and JBTS phenotype are homozygous for this variant. In summary, this seemingly synonymous variant affect splicing and should be considered as likely pathogenic. - |
Jeune thoracic dystrophy Pathogenic:1
Likely pathogenic, criteria provided, single submitter | research | Rare Disease Group, Clinical Genetics, Karolinska Institutet | May 01, 2018 | - - |
Orofaciodigital syndrome XV Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital | Dec 13, 2024 | The homozygous synonymous variant identified in KIAA0753 gene is absent form normal population database fulfilling PM2 and it reported in four deceased patients in homozygous state in clinvar with variation ID: 224512 fulfilling PM3. This synonymous variant has been shown to affect splicing, leading to skipping of exon 4 in the KIAA0753 protein[PMID: 29138412] hence classified as likely pathogenic - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at