rs587777740
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_001024613.4(FEZF1):c.653del(p.Phe218SerfsTer13) variant causes a frameshift 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). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
FEZF1
NM_001024613.4 frameshift
NM_001024613.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.92
Genes affected
FEZF1 (HGNC:22788): (FEZ family zinc finger 1) This gene encodes a transcriptional repressor that belongs to the zinc finger double domain protein family. The encoded protein is thought to play a role in the embryonic migration of gonadotropin-releasing hormone neurons into the brain. Mutations in this gene are associated with hypogonadotropic hypogonadism-22 with anosmia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 7-122303784-GA-G is Pathogenic according to our data. Variant chr7-122303784-GA-G is described in ClinVar as [Pathogenic]. Clinvar id is 156220.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FEZF1 | NM_001024613.4 | c.653del | p.Phe218SerfsTer13 | frameshift_variant | 1/4 | ENST00000442488.7 | |
FEZF1-AS1 | NR_036484.1 | n.130del | non_coding_transcript_exon_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FEZF1 | ENST00000442488.7 | c.653del | p.Phe218SerfsTer13 | frameshift_variant | 1/4 | 1 | NM_001024613.4 | P2 | |
FEZF1 | ENST00000427185.2 | c.503del | p.Phe168SerfsTer13 | frameshift_variant | 2/5 | 1 | A2 | ||
FEZF1-AS1 | ENST00000428449.5 | n.130del | non_coding_transcript_exon_variant | 1/7 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 33
GnomAD4 exome
Cov.:
33
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Hypogonadotropic hypogonadism 22 with anosmia Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 04, 2014 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at