NM_007241.4(SNF8):c.236C>T (p.Pro79Leu) AND Developmental and epileptic encephalopathy 115

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 10, 2024
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003993691.1

Allele description [Variation Report for NM_007241.4(SNF8):c.236C>T (p.Pro79Leu)]

NM_007241.4(SNF8):c.236C>T (p.Pro79Leu)

Gene:

SNF8:SNF8 subunit of ESCRT-II [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q21.32

Genomic location:

Preferred name:

NM_007241.4(SNF8):c.236C>T (p.Pro79Leu)

HGVS:

NC_000017.11:g.48940932G>A
NM_001317192.2:c.236C>T
NM_001317193.2:c.185C>T
NM_001317194.2:c.-167C>T
NM_007241.4:c.236C>TMANE SELECT
NP_001304121.1:p.Pro79Leu
NP_001304122.1:p.Pro62Leu
NP_009172.2:p.Pro79Leu
NC_000017.10:g.47018294G>A
NR_133679.2:n.344C>T

Protein change:

P62L; PRO79LEU

Links:

OMIM: 610904.0003

Molecular consequence:

NM_001317194.2:c.-167C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317192.2:c.236C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001317193.2:c.185C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_007241.4:c.236C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_133679.2:n.344C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Developmental and epileptic encephalopathy 115
Identifiers:: MONDO: MONDO:0968946; MedGen: CN377534; OMIM: 620783

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PEX14 peroxisomal biogenesis factor 14 [Homo sapiens]
PEX14 peroxisomal biogenesis factor 14 [Homo sapiens]
Gene ID:5195

Gene
Igf2bp3 insulin-like growth factor 2 mRNA binding protein 3 [Mus musculus]
Igf2bp3 insulin-like growth factor 2 mRNA binding protein 3 [Mus musculus]
Gene ID:140488

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004812197	OMIM	no assertion criteria provided	Pathogenic (Apr 10, 2024)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004812197

OMIM

no assertion criteria provided

Pathogenic
(Apr 10, 2024)

germline

literature only

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Bi-allelic variants in SNF8 cause a disease spectrum ranging from severe developmental and epileptic encephalopathy to syndromic optic atrophy.

Brugger M, Lauri A, Zhen Y, Gramegna LL, Zott B, Sekulić N, Fasano G, Kopajtich R, Cordeddu V, Radio FC, Mancini C, Pizzi S, Paradisi G, Zanni G, Vasco G, Carrozzo R, Palombo F, Tonon C, Lodi R, La Morgia C, Arelin M, Blechschmidt C, et al.

Am J Hum Genet. 2024 Mar 7;111(3):594-613. doi: 10.1016/j.ajhg.2024.02.005. Epub 2024 Feb 28.

PubMed [citation]

PMID:: 38423010
PMCID:: PMC10940020

Details of each submission

From OMIM, SCV004812197.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

Developmental and Epileptic Encephalopathy 115

For discussion of the c.236C-T transition (c.236C-T, NM_007241.4) in the SNF8 gene, resulting in a pro79-to-leu (P79L) substitution, that was identified in compound heterozygous state in a patient (patient B1) with developmental and epileptic encephalopathy-115 (DEE115; 620783) by Brugger et al. (2024), see 610904.0001.

Neurodevelopmental Disorder Plus Optic Atrophy

In a patient (Patient F1) with neurodevelopmental disorder plus optic atrophy (NEDOA; 620784), Brugger et al. (2024) identified compound heterozygosity for 2 mutations in the SNF8 gene, P79L and a c.304G-A transition, resulting in a val102-to-ile (V102I; 610904.0005) substitution. The mutations were identified by trio whole-exome sequencing. The V102I mutation was present in the gnomAD database (v4.0.0) at an allele frequency of 0.0001691, with 1 homozygote reported.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 23, 2024

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