rs1553182964

Variant names:

• chr1-61404169-CCTTA-C
• rs1553182964
• NM_001134673.4:c.1145_1148delACTT

Variant summary

Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_001134673.4(NFIA):​c.1145_1148delACTT​(p.Tyr382SerfsTer14) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. Y382Y) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 33)
• Consequence: NFIA NM_001134673.4 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 8.91
• Publications: 0 publications found

Genes affected

NFIA (HGNC:7784): (nuclear factor I A) This gene encodes a member of the NF1 (nuclear factor 1) family of transcription factors. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

NFIA Gene-Disease associations (from GenCC):

• brain malformations with or without urinary tract defects

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen
• chromosome 1p32-p31 deletion syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Illumina, Ambry Genetics

ACMG classification

Our verdict: Pathogenic. The variant received 12 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 1-61404169-CCTTA-C is Pathogenic according to our data. Variant chr1-61404169-CCTTA-C is described in ClinVar as Pathogenic. ClinVar VariationId is 521252.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001134673.4. 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
	NFIA	NM_001134673.4	MANE Select	c.1145_1148delACTT	p.Tyr382SerfsTer14	frameshift	Exon 8 of 11	NP_001128145.1	Q12857-1
	NFIA	NM_001145512.2		c.1280_1283delACTT	p.Tyr427SerfsTer14	frameshift	Exon 9 of 12	NP_001138984.1	Q12857-4
	NFIA	NM_001145511.2		c.1121_1124delACTT	p.Tyr374SerfsTer14	frameshift	Exon 8 of 11	NP_001138983.1	Q12857-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFIA	ENST00000403491.8	TSL:1 MANE Select	c.1145_1148delACTT	p.Tyr382SerfsTer14	frameshift	Exon 8 of 11	ENSP00000384523.3	Q12857-1
	NFIA	ENST00000371187.7	TSL:1	c.1145_1148delACTT	p.Tyr382SerfsTer14	frameshift	Exon 8 of 10	ENSP00000360229.3	Q12857-2
	NFIA	ENST00000371189.8	TSL:2	c.1280_1283delACTT	p.Tyr427SerfsTer14	frameshift	Exon 9 of 12	ENSP00000360231.3	Q12857-4

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
1	-	-	Inborn genetic diseases (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		8.9
Mutation Taster		=0/200	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: rs1553182964; hg19: chr1-61869841;