rs121912619
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM1PP5
The NM_016180.5(SLC45A2):āc.1082T>Cā(p.Leu361Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,614,090 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. L361L) has been classified as Likely benign.
Frequency
Consequence
NM_016180.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC45A2 | NM_016180.5 | c.1082T>C | p.Leu361Pro | missense_variant | 5/7 | ENST00000296589.9 | |
SLC45A2 | NM_001012509.4 | c.1082T>C | p.Leu361Pro | missense_variant | 5/6 | ||
SLC45A2 | XM_047417259.1 | c.842T>C | p.Leu281Pro | missense_variant | 5/7 | ||
SLC45A2 | NM_001297417.4 | c.*24T>C | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC45A2 | ENST00000296589.9 | c.1082T>C | p.Leu361Pro | missense_variant | 5/7 | 1 | NM_016180.5 | P1 | |
SLC45A2 | ENST00000382102.7 | c.1082T>C | p.Leu361Pro | missense_variant | 5/6 | 1 | |||
SLC45A2 | ENST00000509381.1 | c.*24T>C | 3_prime_UTR_variant | 4/4 | 1 | ||||
SLC45A2 | ENST00000510600.1 | c.557T>C | p.Leu186Pro | missense_variant | 4/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251472Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135912
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461878Hom.: 0 Cov.: 35 AF XY: 0.0000330 AC XY: 24AN XY: 727244
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74360
ClinVar
Submissions by phenotype
not provided Pathogenic:1Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 09, 2014 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Nov 13, 2023 | This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 361 of the SLC45A2 protein (p.Leu361Pro). This variant is present in population databases (rs121912619, gnomAD 0.01%). This missense change has been observed in individual(s) with clinical features of oculocutaneous albinism (PMID: 14722913, 29345414, 34078970; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 4499). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt SLC45A2 protein function with a negative predictive value of 80%. For these reasons, this variant has been classified as Pathogenic. - |
Oculocutaneous albinism type 4 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 01, 2004 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at