NM_000388.4:c.1622A>T
Variant summary
Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2PP2
The NM_000388.4(CASR):c.1622A>T(p.Asn541Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,884 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N541S) has been classified as Likely benign.
Frequency
Consequence
NM_000388.4 missense
Scores
Clinical Significance
Conservation
Publications
- autosomal dominant hypocalcemia 1Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Illumina, ClinGen, Labcorp Genetics (formerly Invitae)
- familial hypocalciuric hypercalcemia 1Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Illumina, Orphanet, Genomics England PanelApp
- neonatal severe primary hyperparathyroidismInheritance: AR, AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, ClinGen, Labcorp Genetics (formerly Invitae)
- autosomal dominant hypocalcemiaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- epilepsy, idiopathic generalized, susceptibility to, 8Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
- epilepsyInheritance: AD Classification: NO_KNOWN Submitted by: ClinGen
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ACMG classification
Our verdict: Uncertain_significance. The variant received 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CASR | ENST00000639785.2 | c.1622A>T | p.Asn541Ile | missense_variant | Exon 6 of 7 | 1 | NM_000388.4 | ENSP00000491584.2 | ||
CASR | ENST00000498619.4 | c.1652A>T | p.Asn551Ile | missense_variant | Exon 6 of 7 | 1 | ENSP00000420194.1 | |||
CASR | ENST00000638421.1 | c.1622A>T | p.Asn541Ile | missense_variant | Exon 6 of 7 | 5 | ENSP00000492190.1 | |||
CASR | ENST00000490131.7 | c.1391A>T | p.Asn464Ile | missense_variant | Exon 4 of 5 | 5 | ENSP00000418685.2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461884Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727242 show subpopulations
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at