NM_032228.6:c.495_507delAGTAGTCTATCCAinsT

Variant names:

• chr11-13708029-AGTAGTCTATCCA-T
• rs727502796
• NM_032228.6:c.495_507delAGTAGTCTATCCAinsT

Variant summary

Our verdict is Uncertain significance. The variant received 5 ACMG points: 5P and 0B. PM4 PP3 PP5_Moderate

The NM_032228.6(FAR1):​c.495_507delAGTAGTCTATCCAinsT​(p.Glu165_Pro169delinsAsp) variant causes a missense, conservative inframe deletion change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely pathogenic (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: FAR1 NM_032228.6 missense, conservative_inframe_deletion
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 9.32
• Publications: 2 publications found

Genes affected

FAR1 (HGNC:26222): (fatty acyl-CoA reductase 1) The protein encoded by this gene is required for the reduction of fatty acids to fatty alcohols, a process that is required for the synthesis of monoesters and ether lipids. NADPH is required as a cofactor in this reaction, and 16-18 carbon saturated and unsaturated fatty acids are the preferred substrate. This is a peroxisomal membrane protein, and studies suggest that the N-terminus contains a large catalytic domain located on the outside of the peroxisome, while the C-terminus is exposed to the matrix of the peroxisome. Studies indicate that the regulation of this protein is dependent on plasmalogen levels. Mutations in this gene have been associated with individuals affected by severe intellectual disability, early-onset epilepsy, microcephaly, congenital cataracts, growth retardation, and spasticity (PMID: 25439727). A pseudogene of this gene is located on chromosome 13. [provided by RefSeq, Jan 2015]

FAR1 Gene-Disease associations (from GenCC):

• fatty acyl-CoA reductase 1 deficiency

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet, ClinGen, G2P, Labcorp Genetics (formerly Invitae)
• spastic paraparesis-cataracts-speech delay syndrome

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• fatty acyl-CoA reductase 1 upregulation

  Inheritance: AD Classification: MODERATE Submitted by: ClinGen
• hereditary spastic paraplegia 9A

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 5 ACMG points.

• PM4: Nonframeshift variant in NON repetitive region in NM_032228.6.
• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
• PP5: Variant 11-13708029-AGTAGTCTATCCA-T is Pathogenic according to our data. Variant chr11-13708029-AGTAGTCTATCCA-T is described in ClinVar as Likely_pathogenic. ClinVar VariationId is 162212.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032228.6. 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
	FAR1	NM_032228.6	MANE Select	c.495_507delAGTAGTCTATCCAinsT	p.Glu165_Pro169delinsAsp	missense conservative_inframe_deletion	Exon 4 of 12	NP_115604.1	Q8WVX9
	FAR1	NM_001441242.1		c.495_507delAGTAGTCTATCCAinsT	p.Glu165_Pro169delinsAsp	missense conservative_inframe_deletion	Exon 4 of 12	NP_001428171.1
	FAR1	NM_001441243.1		c.495_507delAGTAGTCTATCCAinsT	p.Glu165_Pro169delinsAsp	missense conservative_inframe_deletion	Exon 4 of 12	NP_001428172.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAR1	ENST00000354817.8	TSL:1 MANE Select	c.495_507delAGTAGTCTATCCAinsT	p.Glu165_Pro169delinsAsp	missense conservative_inframe_deletion	Exon 4 of 12	ENSP00000346874.3	Q8WVX9
	FAR1	ENST00000907330.1		c.495_507delAGTAGTCTATCCAinsT	p.Glu165_Pro169delinsAsp	missense conservative_inframe_deletion	Exon 4 of 12	ENSP00000577389.1
	FAR1	ENST00000907331.1		c.495_507delAGTAGTCTATCCAinsT	p.Glu165_Pro169delinsAsp	missense conservative_inframe_deletion	Exon 5 of 13	ENSP00000577390.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Likely pathogenic

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
2	-	-	Fatty acyl-CoA reductase 1 deficiency (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		9.3
Mutation Taster		=7/193	disease causing (long InDel)

Splicing

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

Other links and lift over

dbSNP: rs727502796; hg19: chr11-13729576;