rs80338773
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_080669.6(SLC46A1):c.1126C>T(p.Arg376Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000192 in 1,613,522 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R376Q) has been classified as Likely pathogenic.
Frequency
Consequence
NM_080669.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC46A1 | NM_080669.6 | c.1126C>T | p.Arg376Trp | missense_variant | 3/5 | ENST00000612814.5 | |
SARM1 | NM_015077.4 | c.*5991G>A | 3_prime_UTR_variant | 9/9 | ENST00000585482.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC46A1 | ENST00000612814.5 | c.1126C>T | p.Arg376Trp | missense_variant | 3/5 | 2 | NM_080669.6 | P1 | |
SARM1 | ENST00000585482.6 | c.*5991G>A | 3_prime_UTR_variant | 9/9 | 1 | NM_015077.4 | P1 | ||
SLC46A1 | ENST00000618626.1 | c.1082-1511C>T | intron_variant | 1 | |||||
SLC46A1 | ENST00000582735.1 | c.206+2339C>T | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000325 AC: 8AN: 246220Hom.: 0 AF XY: 0.0000523 AC XY: 7AN XY: 133784
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461244Hom.: 0 Cov.: 30 AF XY: 0.0000330 AC XY: 24AN XY: 726870
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152278Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74448
ClinVar
Submissions by phenotype
Congenital defect of folate absorption Pathogenic:1Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 15, 2007 | - - |
not provided Other:1
not provided, no classification provided | literature only | UniProtKB/Swiss-Prot | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at