Variant chr5-131187053-A-AATT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4_SupportingPP5

The NM_181705.4(LYRM7):c.193_195dupTTA(p.Leu66dup) variant causes a conservative inframe insertion change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).

Frequency

Genomes: not found (cov: 32)

Consequence

LYRM7
NM_181705.4 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 4.12

Variant links:

Genes affected

LYRM7 (HGNC:28072): (LYR motif containing 7) Inner mitochondrial membrane complex III (CIII) is the main enzyme complex in the mitochondrial respiratory chain, and Rieske Fe-S protein (UQCRFS1) is the last catalytic subunit added to the complex. The protein encoded by this gene is a nuclear-encoded mitochondrial matrix protein that stabilizes UQCRFS1 and chaperones it to the CIII complex. Defects in this gene are a cause of mitochondrial complex III deficiency, nuclear type 8. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jun 2014]

LYRM7 links:

HINT1 (HGNC:):

HINT1 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PM4

Nonframeshift variant in NON repetitive region in NM_181705.4. Strenght limited to Supporting due to length of the change: 1aa.

PP5

Variant 5-131187053-A-AATT is Pathogenic according to our data. Variant chr5-131187053-A-AATT is described in ClinVar as [Pathogenic]. Clinvar id is 223135.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LYRM7	NM_181705.4 linkuse as main transcript	c.193_195dupTTA	p.Leu66dup	conservative_inframe_insertion	4/5	ENST00000379380.9	NP_859056.2	Q5U5X0
LYRM7	NM_001293735.2 linkuse as main transcript	c.162+4759_162+4761dupTTA		intron_variant			NP_001280664.1	D6RBV5
LYRM7	NR_121658.2 linkuse as main transcript	n.168+6891_168+6893dupTTA		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
LYRM7	ENST00000379380.9 linkuse as main transcript	c.193_195dupTTA	p.Leu66dup	conservative_inframe_insertion	4/5	1	NM_181705.4	ENSP00000368688.4	Q5U5X0
LYRM7	ENST00000507584.1 linkuse as main transcript	c.162+4759_162+4761dupTTA		intron_variant		2		ENSP00000423991.1	D6RBV5
LYRM7	ENST00000510516.5 linkuse as main transcript	c.91+6891_91+6893dupTTA		intron_variant		2		ENSP00000423283.1	D6R994
HINT1	ENST00000506207.2 linkuse as main transcript	n.109-15323_109-15321dupAAT		intron_variant		5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Mitochondrial complex III deficiency nuclear type 8

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Nov 27, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over