rs137853158
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_000338.3(SLC12A1):c.814G>T(p.Val272Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. V272A) has been classified as Uncertain significance.
Frequency
Consequence
NM_000338.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC12A1 | NM_000338.3 | c.814G>T | p.Val272Phe | missense_variant | 6/27 | ENST00000380993.8 | |
LOC128966560 | XR_932204.4 | n.222+678C>A | intron_variant, non_coding_transcript_variant | ||||
SLC12A1 | NM_001184832.2 | c.814G>T | p.Val272Phe | missense_variant | 6/27 | ||
SLC12A1 | NM_001384136.1 | c.814G>T | p.Val272Phe | missense_variant | 6/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC12A1 | ENST00000380993.8 | c.814G>T | p.Val272Phe | missense_variant | 6/27 | 5 | NM_000338.3 | A1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Bartter disease type 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 1996 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at