2-96761060-CTGGCGGCGCCGGTGCTGCTGGTGCTGCTGTGGGCGCTGGGGGCCCGGGGCCAGGGCAGCCCCCAGCAGGGCACGATCGTGGGCA-C
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM4PP5
The NM_020184.4(CNNM4):c.64_147del(p.Ala22_Met49del) variant causes a inframe deletion 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 (no stars).
Frequency
Genomes: not found (cov: 31)
Consequence
CNNM4
NM_020184.4 inframe_deletion
NM_020184.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.25
Genes affected
CNNM4 (HGNC:105): (cyclin and CBS domain divalent metal cation transport mediator 4) This gene encodes a member of the ancient conserved domain containing protein family. Members of this protein family contain a cyclin box motif and have structural similarity to the cyclins. The encoded protein may play a role in metal ion transport. Mutations in this gene are associated with Jalili syndrome which consists of cone-rod dystrophy and amelogenesis imperfecta. [provided by RefSeq, Feb 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_020184.4.
PP5
Variant 2-96761060-CTGGCGGCGCCGGTGCTGCTGGTGCTGCTGTGGGCGCTGGGGGCCCGGGGCCAGGGCAGCCCCCAGCAGGGCACGATCGTGGGCA-C is Pathogenic according to our data. Variant chr2-96761060-CTGGCGGCGCCGGTGCTGCTGGTGCTGCTGTGGGCGCTGGGGGCCCGGGGCCAGGGCAGCCCCCAGCAGGGCACGATCGTGGGCA-C is described in ClinVar as [Pathogenic]. Clinvar id is 2853.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr2-96761060-CTGGCGGCGCCGGTGCTGCTGGTGCTGCTGTGGGCGCTGGGGGCCCGGGGCCAGGGCAGCCCCCAGCAGGGCACGATCGTGGGCA-C is described in Lovd as [Likely_pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNNM4 | NM_020184.4 | c.64_147del | p.Ala22_Met49del | inframe_deletion | 1/7 | ENST00000377075.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNNM4 | ENST00000377075.3 | c.64_147del | p.Ala22_Met49del | inframe_deletion | 1/7 | 1 | NM_020184.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Jalili syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 01, 2009 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.