rs104894118
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM5PP3_StrongPP5
The NM_004959.5(NR5A1):c.764G>T(p.Arg255Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000808 in 1,609,834 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. R255C) has been classified as Likely pathogenic.
Frequency
Consequence
NM_004959.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NR5A1 | NM_004959.5 | c.764G>T | p.Arg255Leu | missense_variant | 4/7 | ENST00000373588.9 | NP_004950.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NR5A1 | ENST00000373588.9 | c.764G>T | p.Arg255Leu | missense_variant | 4/7 | 1 | NM_004959.5 | ENSP00000362690.4 | ||
NR5A1 | ENST00000620110.4 | c.764G>T | p.Arg255Leu | missense_variant | 4/6 | 5 | ENSP00000483309.1 | |||
NR5A1 | ENST00000373587.3 | c.116G>T | p.Arg39Leu | missense_variant | 2/5 | 3 | ENSP00000362689.3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000164 AC: 4AN: 243268Hom.: 0 AF XY: 0.0000225 AC XY: 3AN XY: 133094
GnomAD4 exome AF: 0.00000823 AC: 12AN: 1457596Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 724666
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152238Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74366
ClinVar
Submissions by phenotype
ADRENAL INSUFFICIENCY, NR5A1-RELATED Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 01, 2000 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at