Is SPG7 c.1663+9G>A pathogenic?

SPG7 c.1663+9G>A is classified Likely benign in SPG7 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-07-23). Ultra-rare (popmax 0.0189%, nfe); Associated with hereditary spastic paraplegia 7.

What condition is associated with SPG7 c.1663+9G>A?

SPG7 c.1663+9G>A is associated with hereditary spastic paraplegia 7 (ClinVar).

How common is SPG7 c.1663+9G>A in the general population?

SPG7 c.1663+9G>A is ultra-rare (popmax 0.0189%, nfe) (gnomAD).

How is Spastic paraplegia type 7 inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

SPG7 c.1663+9G>A

rs756489401 · VCV1135951

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0189%, nfe)

Conditions

hereditary spastic paraplegia 7

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +9	near-intronic (+9 nt from the splice site)
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.24 · evaluated, not missing
Constraint at this position
Conservation	phyloP -2.7	GERP -3.3
Overall
CADD	0.581	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0189% European (non-Finnish) · 220/1,165,436 alleles

Filtering AF 0.0168% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.016%

Overall 0.0144% 229/1,586,900 alleles · ultra-rare exomes 219/1,434,654 · genomes 10/152,246 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0189%	5,297
Finnishnot grpmax-eligible	0.00567%	17,650
African / African-American	0.00402%	24,863
Remaining individualsnot grpmax-eligible	0.00323%	30,935
Admixed American	0.00167%	59,978

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: SPG7
Coding: c.1663+9G>A
MANE Select: NM_003119
dbSNP: rs756489401
Type: single nucleotide variant
Location: chr16:89548122 (GRCh38)
Gene constraint: LOEUF 1.547 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 74.10 · 2 PDB

Full SPG7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary spastic paraplegia 7 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Spastic paraplegia type 7 (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive
Onset: Adolescent, Adult, Childhood, Elderly

Similar variants

SPG7 c.1324+2T>G Pathogenic/Likely pathogenic ★★ same condition
SPG7 c.1552+1G>T Pathogenic/Likely pathogenic ★★ same condition
SPG7 c.1553-2A>G Pathogenic/Likely pathogenic ★★ same condition
SPG7 c.1779+1G>T Pathogenic/Likely pathogenic ★★ same condition
SPG7 c.1936+2T>A Likely pathogenic ★★ same condition
SPG7 c.1937-2A>G Pathogenic ★★ same condition
SPG7 c.2104-2A>G Pathogenic/Likely pathogenic ★★ same condition
SPG7 c.286+1G>T Likely pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/spg7-c-1663-plus-9g-a (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown