LOINC
Version 2.70

97654-8SMN2 gene copy number in Blood or Tissue by Molecular genetics methodActive

Term Description

The SMN2 copy number varies from 0 to 3 copies in the population, with about 10–15% of unaffected individuals having no SMN2 gene. The SMN2 copy number does not impact the carrier status but rather influences severity of disease in patients with spinal muscular atrophy (SMA), where the presence of more copies is associated with milder disease.[PMID: 21673580]
Source: Regenstrief LOINC

Part Description

LP426531-2   SMN2 gene copy number
The SMN2 gene (survival of motor neuron 2, centromeric) [HGNC Gene ID:11118] is located on chromosome 5q13.2. This gene is part of a 500 kb inverted duplication on chromosome 5q13. This duplicated region contains at least four genes and repetitive elements which make it prone to rearrangements and deletions. The repetitiveness and complexity of the sequence have also caused difficulty in determining the organization of this genomic region. The telomeric and centromeric copies of this gene are nearly identical and encode the same protein. While mutations in the telomeric copy are associated with spinal muscular atrophy, mutations in this gene, the centromeric copy, do not lead to disease. This gene may be a modifier of disease caused by mutation in the telomeric copy. The critical sequence difference between the two genes is a single nucleotide in exon 7, which is thought to be an exon splice enhancer. Note that the nine exons of both the telomeric and centromeric copies are designated historically as exon 1, 2a, 2b, and 3-8. It is thought that gene conversion events may involve the two genes, leading to varying copy numbers of each gene. The full length protein encoded by this gene localizes to both the cytoplasm and the nucleus. Within the nucleus, the protein localizes to subnuclear bodies called gems which are found near coiled bodies containing high concentrations of small ribonucleoproteins (snRNPs). This protein forms heteromeric complexes with proteins such as SIP1 and GEMIN4, and also interacts with several proteins known to be involved in the biogenesis of snRNPs, such as hnRNP U protein and the small nucleolar RNA binding protein. Four transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Sep 2008] [NCBI Gene ID:6607] Source: National Center for Biotechnology Information (NCBI) Gene

Fully-Specified Name

Component
SMN2 gene copy number
Property
EntNum
Time
Pt
System
Bld/Tiss
Scale
Qn
Method
Molgen

Additional Names

Short Name
SMN2 copy num EntNum Bld/T
Display Name
SMN2 copy num Molgen (Bld/Tiss) [Entitic number]
Consumer Name Alpha
SMN2 copy number, Blood or tissue specimen

Basic Attributes

Class
MOLPATH
Type
Laboratory
First Released
Version 2.70
Last Updated
Version 2.70
Order vs. Observation
Both

Member of these Panels

LOINC Long Common Name
54089-8 Newborn screening panel American Health Information Community (AHIC)

Example Units

Unit Source
{#} Example UCUM Units

LOINC FHIR® API Example - CodeSystem Request Get Info

https://fhir.loinc.org/CodeSystem/$lookup?system=http://loinc.org&code=97654-8