NM_005055.5(RAPSN):c.-210A>G AND multiple conditions

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jan 25, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000664547.6

Allele description [Variation Report for NM_005055.5(RAPSN):c.-210A>G]

NM_005055.5(RAPSN):c.-210A>G

Gene:

RAPSN:receptor associated protein of the synapse [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11p11.2

Genomic location:

Preferred name:

NM_005055.5(RAPSN):c.-210A>G

Other names:

-38A>G

HGVS:

NC_000011.10:g.47449174T>C
NG_008312.2:g.4962A>G
NM_005055.5:c.-210A>GMANE SELECT
NC_000011.9:g.47470726T>C
NG_008312.1:g.5005A>G
NM_005055.4:c.-210A>G

Note:

NCBI staff reviewed the sequence information reported in PubMed 12651869 Fig. 4B to determine the location of this allele on the current reference sequence.

Nucleotide change:

-38A-G

Links:

OMIM: 601592.0006; dbSNP: rs786200905

NCBI 1000 Genomes Browser:

rs786200905

Condition(s)

Name:: Fetal akinesia deformation sequence 1 (FADS1)
Synonyms:: Pena Shokeir syndrome, type 1; Lethal Pena-Shokeir 1 syndrome; Pena-Shokeir syndrome type I; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0100101; MedGen: C1276035; Orphanet: 994; OMIM: 208150; Human Phenotype Ontology: HP:0001989

Name:: Congenital myasthenic syndrome 11
Synonyms:: MYASTHENIC SYNDROME, CONGENITAL, Ie; Myasthenic syndrome, congenital, 11, associated with acetylcholine receptor deficiency
Identifiers:: MONDO: MONDO:0014588; MedGen: C4225367; Orphanet: 590; OMIM: 616326

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000788529	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Pathogenic (Jun 7, 2017)	unknown	clinical testing	PubMed (5) [See all records that cite these PMIDs] 15145336, 22326364, 19620612, 12651869, 15282317 Citation Link,
SCV000939948	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 25, 2024)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 15145336, 19620612, 22326364, 12651869, 15282317, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000788529

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Pathogenic
(Jun 7, 2017)

unknown

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

Citation Link,

SCV000939948

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 25, 2024)

germline

clinical testing

PubMed (6)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Distinct phenotypes of congenital acetylcholine receptor deficiency.

Burke G, Cossins J, Maxwell S, Robb S, Nicolle M, Vincent A, Newsom-Davis J, Palace J, Beeson D.

Neuromuscul Disord. 2004 Jun;14(6):356-64.

PubMed [citation]

PMID:: 15145336

Myasthenic syndrome due to defects in rapsyn: Clinical and molecular findings in 39 patients.

Milone M, Shen XM, Selcen D, Ohno K, Brengman J, Iannaccone ST, Harper CM, Engel AG.

Neurology. 2009 Jul 21;73(3):228-35. doi: 10.1212/WNL.0b013e3181ae7cbc.

PubMed [citation]

PMID:: 19620612
PMCID:: PMC2715575

See all PubMed Citations (6)

Details of each submission

From Counsyl, SCV000788529.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000939948.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

This variant occurs in a non-coding region of the RAPSN gene. It does not change the encoded amino acid sequence of the RAPSN protein. This variant is present in population databases (rs786200905, gnomAD 0.06%). This variant has been observed in individual(s) with congenital myasthenic syndrome (PMID: 12651869, 15145336, 19620612, 22326364). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 8051). Studies have shown that this variant alters RAPSN gene expression (PMID: 12651869, 15282317). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine