4-118723660-GAAAA-GAAAAAAAAAAAAAA
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014822.4(SEC24D):c.2959-15_2959-6dupTTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Consequence
SEC24D
NM_014822.4 splice_region, intron
NM_014822.4 splice_region, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.471
Genes affected
SEC24D (HGNC:10706): (SEC24 homolog D, COPII coat complex component) The protein encoded by this gene is a member of the SEC24 subfamily of the SEC23/SEC24 family, which is involved in vesicle trafficking. The encoded protein has similarity to yeast Sec24p component of COPII. COPII is the coat protein complex responsible for vesicle budding from the ER. This gene product is implicated in the shaping of the vesicle, and also in cargo selection and concentration. Mutations in this gene have been associated with Cole-Carpenter syndrome, a disorder affecting bone formation, resulting in craniofacial malformations and bones that break easily. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEC24D | NM_014822.4 | c.2959-15_2959-6dupTTTTTTTTTT | splice_region_variant, intron_variant | Intron 22 of 22 | ENST00000280551.11 | NP_055637.2 | ||
SEC24D | NM_001318066.2 | c.2962-15_2962-6dupTTTTTTTTTT | splice_region_variant, intron_variant | Intron 22 of 22 | NP_001304995.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEC24D | ENST00000280551.11 | c.2959-6_2959-5insTTTTTTTTTT | splice_region_variant, intron_variant | Intron 22 of 22 | 1 | NM_014822.4 | ENSP00000280551.6 | |||
SEC24D | ENST00000511481.5 | c.1852-6_1852-5insTTTTTTTTTT | splice_region_variant, intron_variant | Intron 15 of 15 | 1 | ENSP00000425491.1 | ||||
SEC24D | ENST00000502830.1 | n.288-6_288-5insTTTTTTTTTT | splice_region_variant, intron_variant | Intron 1 of 1 | 2 | |||||
SEC24D | ENST00000505134.5 | n.3090-6_3090-5insTTTTTTTTTT | splice_region_variant, intron_variant | Intron 17 of 17 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at