rs1555403942

Positions:

• chr15-40410818-TACACGCTAATCTCACAGTGCAACCACCAACTAAAAGATACCCTCTCCCCTTGGGGGCCAGTCAGACCTGCTTTCTGTAGCATGCTGCCATGAACCAAATGTGGTTAGGAAGGGGCCATGGATTGCTTTAAAATACTTGAGCCAAAAATAATAAAAATAGGACCAGAACTCTTGCATTGAACAACAGACAGACAACATTTGAAGAGAACTCTAAGAAATGGAAGAGTAGGACTAGCTTCCTTTGCAAAGGGAATGGAAAAAGGAGAGGCATTTTCAGCCTTGTAGCCATTGGGCTTAGAAGAGACTTCTAGGACTTTACCGACACCCTGGTCTGAGAGCGAAGTTTGAAGGGGTTTAATGTGGACAGGAAGAGGCAGTACCAGTGAGCTGCTCTAGGGTACTCTGAGGTTGTAACAAGGCCTGTTGGGGGTTTTCCTTGCAGCTGATCAGTGGTGAGTACATCGGAGCCCTGGCCATGAGTGAGCCCAATGCAGGC-TGTTG

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_002225.5(IVD):​c.456+22_510delinsGTTG variant causes a splice acceptor, coding sequence, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: IVD NM_002225.5 splice_acceptor, coding_sequence, intron
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 0.443

Genes affected

IVD (HGNC:6186): (isovaleryl-CoA dehydrogenase) Isovaleryl-CoA dehydrogenase (IVD) is a mitochondrial matrix enzyme that catalyzes the third step in leucine catabolism. The genetic deficiency of IVD results in an accumulation of isovaleric acid, which is toxic to the central nervous system and leads to isovaleric acidemia. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 15-40410819-ACACGCTAATCTCACAGTGCAACCACCAACTAAAAGATACCCTCTCCCCTTGGGGGCCAGTCAGACCTGCTTTCTGTAGCATGCTGCCATGAACCAAATGTGGTTAGGAAGGGGCCATGGATTGCTTTAAAATACTTGAGCCAAAAATAATAAAAATAGGACCAGAACTCTTGCATTGAACAACAGACAGACAACATTTGAAGAGAACTCTAAGAAATGGAAGAGTAGGACTAGCTTCCTTTGCAAAGGGAATGGAAAAAGGAGAGGCATTTTCAGCCTTGTAGCCATTGGGCTTAGAAGAGACTTCTAGGACTTTACCGACACCCTGGTCTGAGAGCGAAGTTTGAAGGGGTTTAATGTGGACAGGAAGAGGCAGTACCAGTGAGCTGCTCTAGGGTACTCTGAGGTTGTAACAAGGCCTGTTGGGGGTTTTCCTTGCAGCTGATCAGTGGTGAGTACATCGGAGCCCTGGCCATGAGTGAGCCCAATGCAGGC-GTTG is Pathogenic according to our data. Variant chr15-40410819-ACACGCTAATCTCACAGTGCAACCACCAACTAAAAGATACCCTCTCCCCTTGGGGGCCAGTCAGACCTGCTTTCTGTAGCATGCTGCCATGAACCAAATGTGGTTAGGAAGGGGCCATGGATTGCTTTAAAATACTTGAGCCAAAAATAATAAAAATAGGACCAGAACTCTTGCATTGAACAACAGACAGACAACATTTGAAGAGAACTCTAAGAAATGGAAGAGTAGGACTAGCTTCCTTTGCAAAGGGAATGGAAAAAGGAGAGGCATTTTCAGCCTTGTAGCCATTGGGCTTAGAAGAGACTTCTAGGACTTTACCGACACCCTGGTCTGAGAGCGAAGTTTGAAGGGGTTTAATGTGGACAGGAAGAGGCAGTACCAGTGAGCTGCTCTAGGGTACTCTGAGGTTGTAACAAGGCCTGTTGGGGGTTTTCCTTGCAGCTGATCAGTGGTGAGTACATCGGAGCCCTGGCCATGAGTGAGCCCAATGCAGGC-GTTG is described in ClinVar as [Pathogenic]. Clinvar id is 459929.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IVD	NM_002225.5	c.456+22_510delinsGTTG		splice_acceptor_variant, coding_sequence_variant, intron_variant	5/12	ENST00000487418.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IVD	ENST00000487418.8	c.456+22_510delinsGTTG		splice_acceptor_variant, coding_sequence_variant, intron_variant	5/12	1	NM_002225.5	P4

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Isovaleryl-CoA dehydrogenase deficiency Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 21, 2023

This variant results in the deletion of part of exon 5 (c.465+22_519delinsGTTG) of the IVD gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in IVD are known to be pathogenic (PMID: 16602101). This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with isovaleric acidemia (PMID: 27904153). ClinVar contains an entry for this variant (Variation ID: 459929). This variant disrupts a region of the IVD protein in which other variant(s) (p.Gly159Ala) have been determined to be pathogenic (PMID: 19099814; Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555403942; hg19: chr15-40703018;