NM_001024613.4:c.653delT

Variant names:

• chr7-122303784-GA-G
• rs587777740
• NM_001024613.4:c.653delT

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2 PP5

The NM_001024613.4(FEZF1):​c.653delT​(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
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 2.92
• Publications: 1 publications found

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]

FEZF1-AS1 (HGNC:41001): (FEZF1 antisense RNA 1)

ENSG00000293696 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 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 VariationId is 156220.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001024613.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FEZF1	NM_001024613.4	MANE Select	c.653delT	p.Phe218SerfsTer13	frameshift	Exon 1 of 4	NP_001019784.2	A0PJY2-1
	FEZF1	NM_001160264.2		c.503delT	p.Phe168SerfsTer13	frameshift	Exon 2 of 5	NP_001153736.1	A0PJY2-2
	FEZF1-AS1	NR_036484.1		n.130delA		non_coding_transcript_exon	Exon 1 of 7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FEZF1	ENST00000442488.7	TSL:1 MANE Select	c.653delT	p.Phe218SerfsTer13	frameshift	Exon 1 of 4	ENSP00000411145.2	A0PJY2-1
	FEZF1	ENST00000427185.2	TSL:1	c.503delT	p.Phe168SerfsTer13	frameshift	Exon 2 of 5	ENSP00000392727.2	A0PJY2-2
	FEZF1	ENST00000914446.1		c.653delT	p.Phe218SerfsTer13	frameshift	Exon 3 of 6	ENSP00000584505.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
1	-	-	Hypogonadotropic hypogonadism 22 with anosmia (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.9
Mutation Taster		=10/190	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs587777740; hg19: chr7-121943838;