6-35498359-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_003322.6(TULP1):c.1597T>C(p.Ser533Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,460,946 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003322.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TULP1 | NM_003322.6 | c.1597T>C | p.Ser533Pro | missense_variant | 15/15 | ENST00000229771.11 | |
LOC124901309 | XR_007059561.1 | n.75+152A>G | intron_variant, non_coding_transcript_variant | ||||
TULP1 | NM_001289395.2 | c.1438T>C | p.Ser480Pro | missense_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TULP1 | ENST00000229771.11 | c.1597T>C | p.Ser533Pro | missense_variant | 15/15 | 1 | NM_003322.6 | P4 | |
TULP1 | ENST00000322263.8 | c.1438T>C | p.Ser480Pro | missense_variant | 14/14 | 1 | A2 | ||
TULP1 | ENST00000614066.4 | c.1591T>C | p.Ser531Pro | missense_variant | 14/14 | 5 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247492Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134452
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460946Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 726770
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Retinitis pigmentosa Uncertain:1
Uncertain significance, criteria provided, single submitter | curation | Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard | Apr 01, 2021 | The p.Ser533Pro variant in TULP1 was identified in an individual with Retinitis pigmentosa, via a collaborative study between the Broad Institute's Center for Mendelian Genomics and the Pierce lab (https://oculargenomics.meei.harvard.edu/labs/pierce-lab/lab-members/). Through a review of available evidence we were able to apply the following criteria: PM2, PP3. Based on this evidence we have classified this variant as a Variant of Uncertain Significance. If you have any questions about the classification please reach out to the Pierce Lab. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at