2-42350663-T-TAAATACACA

Variant names:

• chr2-42350663-T-TAAATACACA
• rs4181
• NM_004718.4:c.*555_*556insTGTGTATTT

Variant summary

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

The NM_004718.4(COX7A2L):​c.*555_*556insTGTGTATTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 0)
• Consequence: COX7A2L NM_004718.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.600
• Publications: 12 publications found

Genes affected

COX7A2L (HGNC:2289): (cytochrome c oxidase subunit 7A2 like) Cytochrome c oxidase (COX), the terminal component of the mitochondrial respiratory chain, catalyzes the electron transfer from reduced cytochrome c to oxygen. This component is a heteromeric complex consisting of 3 catalytic subunits encoded by mitochondrial genes and multiple structural subunits encoded by nuclear genes. The mitochondrially-encoded subunits function in electron transfer, and the nuclear-encoded subunits may function in the regulation and assembly of the complex. This nuclear gene encodes a protein similar to polypeptides 1 and 2 of subunit VIIa in the C-terminal region, and also highly similar to the mouse Sig81 protein sequence. This gene is expressed in all tissues, and upregulated in a breast cancer cell line after estrogen treatment. It is possible that this gene represents a regulatory subunit of COX and mediates the higher level of energy production in target cells by estrogen. Several transcript variants, some protein-coding and others non-protein coding, have been found for this gene. [provided by RefSeq, Jan 2016]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004718.4. 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
	COX7A2L	NM_004718.4	MANE Select	c.*555_*556insTGTGTATTT		3_prime_UTR	Exon 3 of 3	NP_004709.2
	COX7A2L	NM_001319036.1		c.*555_*556insTGTGTATTT		3_prime_UTR	Exon 4 of 4	NP_001305965.1	Q6FGA0
	COX7A2L	NM_001319037.1		c.*555_*556insTGTGTATTT		3_prime_UTR	Exon 3 of 3	NP_001305966.1	Q6FGA0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COX7A2L	ENST00000234301.3	TSL:1 MANE Select	c.*555_*556insTGTGTATTT		3_prime_UTR	Exon 3 of 3	ENSP00000234301.2	O14548
	COX7A2L	ENST00000886112.1		c.*555_*556insTGTGTATTT		3_prime_UTR	Exon 3 of 3	ENSP00000556171.1
	COX7A2L	ENST00000378669.5	TSL:2	c.*555_*556insTGTGTATTT		3_prime_UTR	Exon 4 of 4	ENSP00000367938.1	O14548

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs4181; hg19: chr2-42577803;