NFATC3 p.Thr981Thr

Variant names:

• chr16-68191609-T-T
• NM_173165.3:c.

Your query was ambiguous. Multiple possible variants found:

• chr16-68191610--
• chr16-68191612-G-T
• chr16-68191612-G-C
• chr16-68191612-G-A

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_173165.3(NFATC3):​c. variant causes a exon region change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: NFATC3 NM_173165.3 exon_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.05
• Publications: 0 publications found

Genes affected

NFATC3 (HGNC:7777): (nuclear factor of activated T cells 3) The product of this gene is a member of the nuclear factors of activated T cells DNA-binding transcription complex. This complex consists of at least two components: a preexisting cytosolic component that translocates to the nucleus upon T cell receptor (TCR) stimulation and an inducible nuclear component. Other members of this family participate to form this complex also. The product of this gene plays a role in the regulation of gene expression in T cells and immature thymocytes. Several transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Nov 2010]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173165.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFATC3	NM_173165.3	MANE Select	c.		exon_region	Exon 9 of 10	NP_775188.1	B5B2S1
	NFATC3	NM_004555.4		c.		exon_region	Exon 9 of 11	NP_004546.1	B5B2S0
	NFATC3	NM_173163.3		c.		exon_region	Exon 9 of 11	NP_775186.1	Q12968-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFATC3	ENST00000346183.8	TSL:1 MANE Select	c.		intron	N/A	ENSP00000300659.5	Q12968-1
	NFATC3	ENST00000329524.8	TSL:1	c.		intron	N/A	ENSP00000331324.4	Q12968-2
	NFATC3	ENST00000349223.9	TSL:1	c.		intron	N/A	ENSP00000264008.6	Q12968-3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		4.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr16-68225512;