rs772398324
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Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_205850.3(SLC24A5):c.641delT(p.Leu214fs) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,142 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000055 ( 0 hom. )
Consequence
SLC24A5
NM_205850.3 frameshift
NM_205850.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.61
Genes affected
SLC24A5 (HGNC:20611): (solute carrier family 24 member 5) This gene is a member of the potassium-dependent sodium/calcium exchanger family and encodes an intracellular membrane protein with 2 large hydrophilic loops and 2 sets of multiple transmembrane-spanning segments. Sequence variation in this gene has been associated with differences in skin pigmentation. [provided by RefSeq, Jul 2008]
MYEF2 (HGNC:17940): (myelin expression factor 2) Enables RNA binding activity. Involved in myotube differentiation and neuron differentiation. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 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 15-48136732-CT-C is Pathogenic according to our data. Variant chr15-48136732-CT-C is described in ClinVar as [Pathogenic]. Clinvar id is 440483.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-48136732-CT-C is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC24A5 | NM_205850.3 | c.641delT | p.Leu214fs | frameshift_variant | 6/9 | ENST00000341459.8 | NP_995322.1 | |
MYEF2 | NM_016132.5 | c.*6175delA | 3_prime_UTR_variant | 17/17 | ENST00000324324.12 | NP_057216.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC24A5 | ENST00000341459.8 | c.641delT | p.Leu214fs | frameshift_variant | 6/9 | 1 | NM_205850.3 | ENSP00000341550.3 | ||
SLC24A5 | ENST00000449382.2 | c.461delT | p.Leu154fs | frameshift_variant | 5/8 | 1 | ENSP00000389966.2 | |||
MYEF2 | ENST00000324324.12 | c.*6175delA | 3_prime_UTR_variant | 17/17 | 1 | NM_016132.5 | ENSP00000316950.7 | |||
SLC24A5 | ENST00000463289.1 | n.401delT | non_coding_transcript_exon_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152058Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250358Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135366
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GnomAD4 exome AF: 0.00000548 AC: 8AN: 1461084Hom.: 0 Cov.: 31 AF XY: 0.00000826 AC XY: 6AN XY: 726808
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152058Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74280
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:3
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 27, 2023 | This sequence change creates a premature translational stop signal (p.Leu214Argfs*12) in the SLC24A5 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC24A5 are known to be pathogenic (PMID: 23985994, 26686029). This variant is present in population databases (rs772398324, gnomAD 0.009%). This premature translational stop signal has been observed in individual(s) with clinical features of oculocutaneous albinism (PMID: 23985994). ClinVar contains an entry for this variant (Variation ID: 440483). For these reasons, this variant has been classified as Pathogenic. - |
SLC24A5-related disorder Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 26, 2024 | The SLC24A5 c.641delT variant is predicted to result in a frameshift and premature protein termination (p.Leu214Argfs*12). This variant has been reported in the homozygous state in individuals with oculocutaneous albinism (Morice-Picard et al. 2014. PubMed ID: 23985994). This variant is reported in 0.0087% of alleles in individuals of Latino descent in gnomAD. Frameshift variants in SLC24A5 are expected to be pathogenic. This variant is interpreted as pathogenic. - |
Oculocutaneous albinism type 6 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 21, 2022 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at