rs863225019

Variant names:

• chr2-71526332-A-AGGACTTGCCGCAGAG
• rs863225019
• ENST00000410020.8:c.1230_1231insGGGACTTGCCGCAGA

Variant summary

Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM4 PP5_Moderate

The ENST00000410020.8(DYSF):​c.1230_1231insGGGACTTGCCGCAGA​(p.Gly410_Ala411insGlyThrCysArgArg) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. A411A) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: DYSF ENST00000410020.8 conservative_inframe_insertion
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 0.121
• Publications: 0 publications found

Genes affected

DYSF (HGNC:3097): (dysferlin) The protein encoded by this gene belongs to the ferlin family and is a skeletal muscle protein found associated with the sarcolemma. It is involved in muscle contraction and contains C2 domains that play a role in calcium-mediated membrane fusion events, suggesting that it may be involved in membrane regeneration and repair. In addition, the protein encoded by this gene binds caveolin-3, a skeletal muscle membrane protein which is important in the formation of caveolae. Specific mutations in this gene have been shown to cause autosomal recessive limb girdle muscular dystrophy type 2B (LGMD2B) as well as Miyoshi myopathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2008]

DYSF Gene-Disease associations (from GenCC):

• autosomal recessive limb-girdle muscular dystrophy

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• neuromuscular disease caused by qualitative or quantitative defects of dysferlin

  Inheritance: AR Classification: DEFINITIVE Submitted by: Myriad Women’s Health
• autosomal recessive limb-girdle muscular dystrophy type 2B

  Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
• distal myopathy with anterior tibial onset

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• congenital myopathy, Paradas type

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Miyoshi myopathy

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 4 ACMG points.

• PM4: Nonframeshift variant in NON repetitive region in ENST00000410020.8.
• PP5: Variant 2-71526332-A-AGGACTTGCCGCAGAG is Pathogenic according to our data. Variant chr2-71526332-A-AGGACTTGCCGCAGAG is described in ClinVar as Pathogenic. ClinVar VariationId is 217221.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000410020.8. 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
	DYSF	NM_001130987.2	MANE Select	c.1263_1276+1dupGGACTTGCCGCAGAG		splice_donor intron	N/A	NP_001124459.1
	DYSF	NM_003494.4	MANE Plus Clinical	c.1167_1180+1dupGGACTTGCCGCAGAG		splice_donor intron	N/A	NP_003485.1
	DYSF	NM_001130981.2		c.1260_1273+1dupGGACTTGCCGCAGAG		splice_donor intron	N/A	NP_001124453.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYSF	ENST00000410020.8	TSL:1 MANE Select	c.1230_1231insGGGACTTGCCGCAGA	p.Gly410_Ala411insGlyThrCysArgArg	conservative_inframe_insertion	Exon 13 of 56	ENSP00000386881.3
	DYSF	ENST00000258104.8	TSL:1 MANE Plus Clinical	c.1134_1135insGGGACTTGCCGCAGA	p.Gly378_Ala379insGlyThrCysArgArg	conservative_inframe_insertion	Exon 12 of 55	ENSP00000258104.3
	DYSF	ENST00000409582.7	TSL:1	c.1227_1228insGGGACTTGCCGCAGA	p.Gly409_Ala410insGlyThrCysArgArg	conservative_inframe_insertion	Exon 13 of 56	ENSP00000386547.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions as Germline

Significance: Pathogenic

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
1	-	-	Autosomal recessive limb-girdle muscular dystrophy type 2B (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.12
Mutation Taster		=40/60	disease causing (ClinVar)

Splicing

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

Other links and lift over

dbSNP: rs863225019; hg19: chr2-71753462;