rs397514615

Variant names:

• chr2-227330777-C-T
• rs397514615
• NM_001277062.2:c.112C>T

Variant summary

Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PVS1 PM2 PP5

The NM_001277062.2(MFF):​c.112C>T​(p.Gln38*) 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. Variant has been reported in ClinVar as Likely pathogenic (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MFF NM_001277062.2 stop_gained
• Clinical Significance: Pathogenic/Likely pathogenic no assertion criteria provided P:2
• Conservation: PhyloP100: 1.32
• Publications: 4 publications found

Genes affected

MFF (HGNC:24858): (mitochondrial fission factor) This is a nuclear gene encoding a protein that functions in mitochondrial and peroxisomal fission. The encoded protein recruits dynamin-1-like protein (DNM1L) to mitochondria. There are multiple pseudogenes for this gene on chromosomes 1, 5, and X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2013]

MFF Gene-Disease associations (from GenCC):

• encephalopathy due to defective mitochondrial and peroxisomal fission 2

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• encephalopathy due to mitochondrial and peroxisomal fission defect

  Inheritance: AR Classification: MODERATE Submitted by: ClinGen
• Leigh syndrome

  Inheritance: AR Classification: MODERATE Submitted by: ClinGen

ACMG classification

Our verdict: Pathogenic. The variant received 11 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 2-227330777-C-T is Pathogenic according to our data. Variant chr2-227330777-C-T is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 39831.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001277062.2. 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
	MFF	NM_001277062.2	MANE Select	c.112C>T	p.Gln38*	stop_gained	Exon 3 of 9	NP_001263991.1	Q9GZY8-2
	MFF	NM_001277061.2		c.190C>T	p.Gln64*	stop_gained	Exon 4 of 11	NP_001263990.1	Q9GZY8-1
	MFF	NM_020194.5		c.190C>T	p.Gln64*	stop_gained	Exon 4 of 11	NP_064579.3	Q9GZY8-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MFF	ENST00000304593.14	TSL:2 MANE Select	c.112C>T	p.Gln38*	stop_gained	Exon 3 of 9	ENSP00000304898.10	Q9GZY8-2
	MFF	ENST00000337110.11	TSL:1	c.112C>T	p.Gln38*	stop_gained	Exon 3 of 8	ENSP00000338412.7	Q9GZY8-3
	MFF	ENST00000353339.8	TSL:5	c.190C>T	p.Gln64*	stop_gained	Exon 4 of 11	ENSP00000302037.4	Q9GZY8-1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions

Significance: Pathogenic/Likely pathogenic

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
1	-	-	Encephalopathy due to defective mitochondrial and peroxisomal fission 2 (1)
1	-	-	Mitochondrial encephalomyopathy;C0557874:Global developmental delay (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.29
CADD	Pathogenic	36
DANN	Uncertain	1.0
Eigen	Pathogenic	0.85
Eigen_PC	Pathogenic	0.73
FATHMM_MKL	Benign	0.61	D
PhyloP100		1.3
Vest4		0.71
GERP RS		5.8
Mutation Taster		=1/199	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs397514615; hg19: chr2-228195493;