7-76397688-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_080744.2(SSC4D):c.698G>A(p.Gly233Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,302 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_080744.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SSC4D | NM_080744.2 | c.698G>A | p.Gly233Glu | missense_variant | Exon 6 of 11 | ENST00000275560.4 | NP_542782.1 | |
SSC4D | XM_024446664.2 | c.785G>A | p.Gly262Glu | missense_variant | Exon 7 of 12 | XP_024302432.1 | ||
SSC4D | XM_017011750.2 | c.191G>A | p.Gly64Glu | missense_variant | Exon 3 of 8 | XP_016867239.1 | ||
ZP3 | NM_007155.6 | c.-176C>T | 5_prime_UTR_variant | Exon 1 of 9 | NP_009086.4 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000407 AC: 1AN: 245790Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133940
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461070Hom.: 0 Cov.: 35 AF XY: 0.00000688 AC XY: 5AN XY: 726918
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.698G>A (p.G233E) alteration is located in exon 6 (coding exon 5) of the SSC4D gene. This alteration results from a G to A substitution at nucleotide position 698, causing the glycine (G) at amino acid position 233 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at