17-40093972-A-C

Variant names:

• chr17-40093972-A-C
• rs1987690479
• NM_021724.5:c.1585T>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_021724.5(NR1D1):​c.1585T>G​(p.Ser529Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: NR1D1 NM_021724.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.32

Genes affected

NR1D1 (HGNC:7962): (nuclear receptor subfamily 1 group D member 1) This gene encodes a transcription factor that is a member of the nuclear receptor subfamily 1. The encoded protein is a ligand-sensitive transcription factor that negatively regulates the expression of core clock proteins. In particular this protein represses the circadian clock transcription factor aryl hydrocarbon receptor nuclear translocator-like protein 1 (ARNTL). This protein may also be involved in regulating genes that function in metabolic, inflammatory and cardiovascular processes. [provided by RefSeq, Jan 2013]

THRA (HGNC:11796): (thyroid hormone receptor alpha) The protein encoded by this gene is a nuclear hormone receptor for triiodothyronine. It is one of the several receptors for thyroid hormone, and has been shown to mediate the biological activities of thyroid hormone. Knockout studies in mice suggest that the different receptors, while having certain extent of redundancy, may mediate different functions of thyroid hormone. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.20662701).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NR1D1	NM_021724.5	c.1585T>G	p.Ser529Ala	missense_variant	Exon 7 of 8	ENST00000246672.4	NP_068370.1
THRA	NM_001190919.2	c.*590A>C		downstream_gene_variant			NP_001177848.1
THRA	NM_003250.6	c.*590A>C		downstream_gene_variant			NP_003241.2
THRA	NM_001190918.2	c.*590A>C		downstream_gene_variant			NP_001177847.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NR1D1	ENST00000246672.4	c.1585T>G	p.Ser529Ala	missense_variant	Exon 7 of 8	1	NM_021724.5	ENSP00000246672.3
THRA	ENST00000264637.8	c.*590A>C		downstream_gene_variant		1		ENSP00000264637.4
THRA	ENST00000584985.5	c.*590A>C		downstream_gene_variant		1		ENSP00000463466.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jan 07, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1585T>G (p.S529A) alteration is located in exon 7 (coding exon 7) of the NR1D1 gene. This alteration results from a T to G substitution at nucleotide position 1585, causing the serine (S) at amino acid position 529 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.057
BayesDel_addAF	Uncertain	0.15	D
BayesDel_noAF	Uncertain	-0.030
CADD	Benign	19
DANN	Benign	0.87
DEOGEN2	Uncertain	0.51	D
Eigen	Benign	-0.38
Eigen_PC	Benign	-0.15
FATHMM_MKL	Uncertain	0.79	D
LIST_S2	Benign	0.64	T
M_CAP	Benign	0.025	D
MetaRNN	Benign	0.21	T
MetaSVM	Uncertain	0.18	D
MutationAssessor	Benign	-0.060	N
PrimateAI	Uncertain	0.52	T
PROVEAN	Benign	-0.91	N
REVEL	Uncertain	0.43
Sift	Benign	0.70	T
Sift4G	Benign	0.62	T
Polyphen		0.056	B
Vest4		0.16
MutPred		0.43		Loss of disorder (P = 0.0622);
MVP		0.84
MPC		0.96
ClinPred		0.72	D
GERP RS		5.1
Varity_R		0.30
gMVP		0.082

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1987690479; hg19: chr17-38250225;