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NM_003086.4(SNAPC4):c.1325+1G>T AND Neurodevelopmental disorder with motor regression, progressive spastic paraplegia, and oromotor dysfunction

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 27, 2023
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:
RCV003330119.2

Allele description [Variation Report for NM_003086.4(SNAPC4):c.1325+1G>T]

NM_003086.4(SNAPC4):c.1325+1G>T

Gene:
SNAPC4:small nuclear RNA activating complex polypeptide 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q34.3
Genomic location:
Preferred name:
NM_003086.4(SNAPC4):c.1325+1G>T
HGVS:
  • NC_000009.12:g.136387484C>A
  • NG_051233.1:g.17737G>T
  • NM_001394201.1:c.1325+1G>T
  • NM_001394202.1:c.1325+1G>T
  • NM_001394203.1:c.1325+1G>T
  • NM_003086.4:c.1325+1G>TMANE SELECT
  • NC_000009.11:g.139281936C>A
  • NM_003086.3:c.1325+1G>T
Nucleotide change:
IVS13DS, G-T, +1
Links:
OMIM: 602777.0002
Molecular consequence:
  • NM_001394201.1:c.1325+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001394202.1:c.1325+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001394203.1:c.1325+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_003086.4:c.1325+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Neurodevelopmental disorder with motor regression, progressive spastic paraplegia, and oromotor dysfunction (NEDRSO)
Identifiers:
MONDO: MONDO:0957791; MedGen: CN375537; OMIM: 620515

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004037095OMIM
no assertion criteria provided
Pathogenic
(Sep 27, 2023) 		germlineliterature only

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Bi-allelic SNAPC4 variants dysregulate global alternative splicing and lead to neuroregression and progressive spastic paraparesis.

Frost FG, Morimoto M, Sharma P, Ruaud L, Belnap N, Calame DG, Uchiyama Y, Matsumoto N, Oud MM, Ferreira EA, Narayanan V, Rangasamy S, Huentelman M, Emrick LT, Sato-Shirai I, Kumada S, Wolf NI, Steinbach PJ, Huang Y; Undiagnosed Diseases Network., Pusey BN, Passemard S, et al.

Am J Hum Genet. 2023 Apr 6;110(4):663-680. doi: 10.1016/j.ajhg.2023.03.001. Epub 2023 Mar 24.

PubMed [citation]
PMID:
36965478
PMCID:
PMC10119142

Details of each submission

From OMIM, SCV004037095.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

For discussion of the c.1325+1G-T transversion (c.1325+1G-T, NM_003086.3) in intron 13 of the SNAPC4 gene, resulting in a splicing defect, frameshift, and premature termination (Arg434GlyfsTer10) in the DNA-binding domain, that was found in compound heterozygous state in a patient with neurodevelopmental disorder with motor regression, progressive spastic paraplegia, and oromotor dysfunction (NEDRSO; 620515) by Frost et al. (2023), see 602777.0001.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 14, 2024