NM_014334.4:c.808C>T

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1_ModeratePM2PP5_Very_Strong

The NM_014334.4(FRRS1L):​c.808C>T​(p.Gln270*) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).

Frequency

Genomes: not found (cov: 32)

Consequence

FRRS1L
NM_014334.4 stop_gained

Scores

5
1
1

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:5

Conservation

PhyloP100: 9.60
Variant links:
Genes affected
FRRS1L (HGNC:1362): (ferric chelate reductase 1 like) This gene encodes a component of the outer-core of an alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor protein in the brain. The encoded protein is thought to interact with inner-core components of the receptor, and play a role in the modulation of glutamate signaling. Mutations in this gene are associated with early infantile epileptic encephalopathy 37. [provided by RefSeq, Jul 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 12 ACMG points.

PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.0839 CDS is truncated, and there are 1 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 9-109137529-G-A is Pathogenic according to our data. Variant chr9-109137529-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 218151.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-109137529-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FRRS1LNM_014334.4 linkc.808C>T p.Gln270* stop_gained Exon 5 of 5 ENST00000561981.5 NP_055149.3 Q9P0K9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FRRS1LENST00000561981.5 linkc.808C>T p.Gln270* stop_gained Exon 5 of 5 1 NM_014334.4 ENSP00000477141.2 Q9P0K9
FRRS1LENST00000644747.1 linkn.*426C>T non_coding_transcript_exon_variant Exon 4 of 4 ENSP00000493964.1 A0A2R8Y4E4
FRRS1LENST00000644747.1 linkn.*426C>T 3_prime_UTR_variant Exon 4 of 4 ENSP00000493964.1 A0A2R8Y4E4

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Developmental and epileptic encephalopathy, 37 Pathogenic:4
Aug 05, 2021
Revvity Omics, Revvity
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Oct 23, 2020
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only

- -

Mar 14, 2024
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: research

- -

-
Centogene AG - the Rare Disease Company
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Chorea;C0036572:Seizure;C1838578:Progressive encephalopathy Pathogenic:1
Nov 11, 2015
Kruer lab, Phoenix Children's Hospital
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: research

Leads to loss of protein by immunoblot; leads to impaired co-localization with GluR1 component of AMPA receptor by TIRF; loss of FRRS1L leads to attenuated AMPA currents by electrophysiology -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.63
D
BayesDel_noAF
Pathogenic
0.66
CADD
Pathogenic
40
DANN
Uncertain
1.0
Eigen
Pathogenic
1.1
Eigen_PC
Pathogenic
0.99
FATHMM_MKL
Pathogenic
0.99
D
Vest4
0.30
GERP RS
6.0

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.070
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs878853280; hg19: chr9-111899809; COSMIC: COSV73746916; COSMIC: COSV73746916; API