NM_013387.4:c.25A>T

Variant names:

• chr22-29767423-A-T
• rs771003671
• NM_013387.4:c.25A>T

Variant summary

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

The NM_013387.4(UQCR10):​c.25A>T​(p.Lys9*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: UQCR10 NM_013387.4 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.670
• Publications: 0 publications found

Genes affected

UQCR10 (HGNC:30863): (ubiquinol-cytochrome c reductase, complex III subunit X) UCRC is a subunit of mitochondrial complex III (ubiquinol-cytochrome c reductase; EC 1.10.2.2), which forms the middle segment of the respiratory chain of the inner mitochondrial membrane (Schagger et al., 1995 [PubMed 8592474]).[supplied by OMIM, Mar 2008]

ENSG00000287967 (HGNC:):

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_013387.4. 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
	UQCR10	NM_013387.4	MANE Select	c.25A>T	p.Lys9*	stop_gained	Exon 1 of 2	NP_037519.2
	UQCR10	NM_001003684.2		c.25A>T	p.Lys9*	stop_gained	Exon 1 of 2	NP_001003684.1	Q9UDW1-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UQCR10	ENST00000330029.6	TSL:1 MANE Select	c.25A>T	p.Lys9*	stop_gained	Exon 1 of 2	ENSP00000332887.6	Q9UDW1-1
	UQCR10	ENST00000401406.3	TSL:1	c.25A>T	p.Lys9*	stop_gained	Exon 1 of 2	ENSP00000384962.3	Q9UDW1-2
	UQCR10	ENST00000894363.1		c.25A>T	p.Lys9*	stop_gained	Exon 1 of 2	ENSP00000564422.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.22	D
BayesDel_noAF	Uncertain	0.080
CADD	Pathogenic	34
DANN	Benign	0.96
Eigen	Benign	-0.082
Eigen_PC	Benign	-0.42
FATHMM_MKL	Benign	0.16	N
PhyloP100		0.67
Vest4		0.16
GERP RS		0.60
PromoterAI		0.15	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=33/167	disease causing (fs/PTC)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs771003671; hg19: chr22-30163412;