mice display defects of the periaxonal cytoplasmic
collar in the spinal cord with later oligodendro-cyte degeneration (34). MAG was found mutated in family 1226, displaying a homozygous
Cys430→Gly430 missense mutation.
REEP2 encodes the receptor expression-
enhancing protein 2, a paralog of REEP1, mutated
in SPG31 (35). Family 1967 displays a homozy-
gous Met1→Thr1 mutation in REEP2 removing
the canonical start codon and is mutated in a sec-
ond recessive HSP family in an independent
cohort (36). All of these gene mutations seg-
regated with the phenotype in the family ac-
cording to recessive inheritance and were not
encountered in our exome database, consistent
with pathogenicity. Although further validation
of these three candidates is necessary in larger
cohorts, the data suggest the HSPome can be
useful to identify HSP-relevant pathways and
genes.
Link Between HSP and Neurodegenerative
Disease Genes
Some of the genes we identified in this cohort
have been previously associated with other neurodegenerative disorders (e.g., CLN8, EIF2B5,
and AMPD2) primarily affecting areas of the
nervous system other than the corticospinal tract.
Prompted by this observation, we used the network to examine the similarity of HSP genes
(seed + candidates) to other common neurological disorders. By using the random walk distance, we found that the set of HSP seeds plus
candidates is significantly overlapping with sets
of genes previously implicated in three neurodegenerative disorders, amyotrophic lateral sclerosis (ALS), Alzheimer’s disease, and Parkinson’s
disease (P = 1.1 × 10−02, P = 7.6 × 10−03, P = 1.6 ×
10−02, respectively) (Fig. 4). In contrast, we did
not find a similar association with sets for representative neurodevelopmental disorders such
as autism spectrum disorders and epilepsy (P =
0.49 and P = 0.51, respectively; fig. S12), nor with
nonneurological disorders represented by heart
and pulmonary disorders.
Discussion
By using WES, we identified 18 previously unknown candidates for AR-HSP (fig. S13), three
of which (ERLIN1, KIF1C, and NT5C2) alone
explain almost 20% of this cohort. These new
candidates are predicted to display near 100%
risk of HSP when mutated (37). All mutations were
predicted as damaging to protein function, probably resulting in null or severely reduced function,
consistent with the recessive mode of inheritance.
In about 25% of the families a single candidate
gene mutation could not be identified, probably a
result of two factors: (i) Some mutations are in
noncoding regions. (ii) Some causative mutations
within the exome do not stand out more than
other variants.
Four of our candidate HSP genes are located
within previously identified loci for AR-HSP for
which genes were not known: ENTPD1, NT5C2,
ERLIN1, and MARS. Both ERLIN1 and NT5C2
are in the SPG45 locus (38) and ENTPD1 resides
in SPG27 (39). Recently, the MARS2 gene, encoding a methionyl-tRNA synthetase, was implicated
in the spastic ataxia 3 (SPAX3) phenotype (40).
KIF1C is within the spastic ataxia 2 (SAX2) locus
(41). On the basis of our findings, we returned to
the original SPAX2 family and identified a homozygous deletion of exons 14 to 18, confirming
KIF1C as the SPAX2 gene (fig. S14).
Our data support the idea that rare genetic mutations may converge on a few key biological processes, and our HSP interactome demonstrates that
many of the known and candidate HSP genes are
highly connected. This highlights important biological processes, such as cellular transport, nucleotide
metabolism, and synapse and axon development.
Some of the HSP gene modules suggest potential
Family 1370
Family 1226
BICD2
MAG
H I J
A
BC
1 23 456 7
1 2 3 4
I
II
III
IV
Branch II
Gene
Symbol
Entrez
Gene ID Protein Name
Putative Biological
Function
Family
#
Nucleotide
Change
Deduced
Protein Change Phenotype
Present
in HSPome
BICD2 271 Bicaudal D homolog 2 Protein transport 1370 c. G1823A p. S608L U Yes
MAG 23204
Myelin associated
glycoprotein Component of myelin 1226 c T1288G p. C430G C Yes
12 34 5 6 7
I
II
III
IV
V
1 2
REEP2
I
II
III
IV
REEP2 51308
Receptor accessory
protein 2 ER-shaping protein 1967 c T210C p. M1 T U Yes
Family 1967
DE
FG
PLP1
MAGCCDC64
KIF1C
REEP2
REEP
pLOD
3.00
2.00
1.00
Fig. 3. Genes from HSP networks found mutated in HSP. (A) HSP candidate genes predicted from the
HSPome found mutated in the HSP cohort. BICD2, MAP, and REEP2 were subsequently found mutated in HSP
families 1370 (B), 1226 (D), and 1967 (F), respectively. (C) Homozygosity plot from family 1370. Red bars,
regions of homozygosity; arrow, homozygous block containing BICD2. (E) Linkage plot of family 1226; arrow,
MAG locus. (G) Homozygosity plot; arrow, REEP2 locus. (H to J) Zoom in from HSPome for specific interaction
identifying candidates CCDC64 (a paralog of BIC2D), MAG, and REEP2 (yellow) with previously published
(blue) and newly identified (red) genes mutated in HSP. Blue lines denote manually curated interactions.
