3-23959738-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_005126.5(NR1D2):c.440C>T(p.Ser147Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,606 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005126.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NR1D2 | NM_005126.5 | c.440C>T | p.Ser147Phe | missense_variant | Exon 4 of 8 | ENST00000312521.9 | NP_005117.3 | |
NR1D2 | NM_001145425.2 | c.215C>T | p.Ser72Phe | missense_variant | Exon 4 of 8 | NP_001138897.1 | ||
NR1D2 | XM_006713451.4 | c.440C>T | p.Ser147Phe | missense_variant | Exon 4 of 7 | XP_006713514.1 | ||
NR1D2 | NR_110524.2 | n.733C>T | non_coding_transcript_exon_variant | Exon 4 of 9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NR1D2 | ENST00000312521.9 | c.440C>T | p.Ser147Phe | missense_variant | Exon 4 of 8 | 1 | NM_005126.5 | ENSP00000310006.3 | ||
NR1D2 | ENST00000383773.8 | n.440C>T | non_coding_transcript_exon_variant | Exon 4 of 9 | 1 | ENSP00000373283.3 | ||||
NR1D2 | ENST00000468700.1 | n.335C>T | non_coding_transcript_exon_variant | Exon 3 of 4 | 3 | |||||
NR1D2 | ENST00000492552.5 | n.557C>T | non_coding_transcript_exon_variant | Exon 4 of 8 | 2 | ENSP00000520893.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461606Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727104
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.440C>T (p.S147F) alteration is located in exon 4 (coding exon 4) of the NR1D2 gene. This alteration results from a C to T substitution at nucleotide position 440, causing the serine (S) at amino acid position 147 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.