ENST00000390477.2:c.278-76C>A

Variant names:

• chr14-22463133-A-.
• ENST00000390477.2:c.200A>.

Variant summary

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

The ENST00000390477.2(TRDC):​c.200A>.​(p.Asn67???) variant causes a missense change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 N/A (N/A hom., cov:)
  • Exomes 𝑓: N/A (N/A hom.)
• Consequence: TRDC ENST00000390477.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

TRDC (HGNC:12253): (T cell receptor delta constant) T cell receptors recognize foreign antigens which have been processed as small peptides and bound to major histocompatibility complex (MHC) molecules at the surface of antigen presenting cells (APC). Each T cell receptor is a dimer consisting of one alpha and one beta chain or one delta and one gamma chain. In a single cell, the T cell receptor loci are rearranged and expressed in the order delta, gamma, beta, and alpha. If both delta and gamma rearrangements produce functional chains, the cell expresses delta and gamma. If not, the cell proceeds to rearrange the beta and alpha loci. This region represents the germline organization of the T cell receptor alpha and delta loci. Both the alpha and delta loci include V (variable), J (joining), and C (constant) segments and the delta locus also includes diversity (D) segments. The delta locus is situated within the alpha locus, between the alpha V and J segments. During T cell development, the delta chain is synthesized by a recombination event at the DNA level joining a D segment with a J segment; a V segment is then joined to the D-J gene. The alpha chain is synthesized by recombination joining a single V segment with a J segment. For both chains, the C segment is later joined by splicing at the RNA level. Recombination of many different V segments with several J segments provides a wide range of antigen recognition. Additional diversity is attained by junctional diversity, resulting from the random additional of nucleotides by terminal deoxynucleotidyltransferase. Five variable segments can be used in either alpha or delta chains and are described by TRAV/DV symbols. Several V and J segments of the alpha locus are known to be incapable of encoding a protein and are considered pseudogenes. [provided by RefSeq, Aug 2016]

TRD-AS1 (HGNC:56197): (TRD antisense RNA 1)

TRA (HGNC:12027):

TRD (HGNC:12252):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRDC	unassigned_transcript_2244	c.200A>.	p.Asn67???	missense_variant	Exon 1 of 4
TRA		n.22463133A>.		intragenic_variant
TRD		n.22463133A>.		intragenic_variant
TRD-AS1	NR_148361.1	n.225+18108T>.		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRDC	ENST00000390477.2	c.200A>.	p.Asn67???	missense_variant	Exon 1 of 4	6		ENSP00000451468.1
TRD-AS1	ENST00000556777.2	n.708T>.		non_coding_transcript_exon_variant	Exon 4 of 4	3
TRD-AS1	ENST00000514473.2	n.225+18108T>.		intron_variant	Intron 2 of 2	2

Frequencies

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

We have no GnomAD4 genomes data on this position. Probably position not covered by the project.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr14-22932125;