Is SPATA7 p.Ser210= (c.630C>T) pathogenic?

SPATA7 p.Ser210= (c.630C>T) is classified Likely benign in SPATA7 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-19). Very rare (popmax 0.0022%, sas); Associated with Leber congenital amaurosis 3.

What condition is associated with SPATA7 p.Ser210= (c.630C>T)?

SPATA7 p.Ser210= (c.630C>T) is associated with Leber congenital amaurosis 3 (ClinVar).

How common is SPATA7 p.Ser210= (c.630C>T) in the general population?

SPATA7 p.Ser210= (c.630C>T) is very rare (popmax 0.0022%, sas) (gnomAD).

How is Leber congenital amaurosis inherited?

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

SPATA7 p.Ser210=

c.630C>T · rs1227165374 · VCV1096778

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0022%, sas)

Conditions

Leber congenital amaurosis 3

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.54	GERP 1.1, phastCons 0.69
Overall
CADD	9.932	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0022% South Asian · 2/91,084 alleles

Filtering AF 0.000365% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000137%

Overall 0.000124% 2/1,614,062 alleles · very rare exomes 1/1,461,866 · genomes 1/152,196 · joint denominator

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: SPATA7
Protein: p.Ser210=
Coding: c.630C>T
MANE Select: NM_018418
dbSNP: rs1227165374
Type: single nucleotide variant
Location: chr14:88426489 (GRCh38)
Gene constraint: LOEUF 1.22 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 58.28

Full SPATA7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Leber congenital amaurosis 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Leber congenital amaurosis (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive
Onset: Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

SPATA7 c.94+2T>C Likely pathogenic ★★ same condition
SPATA7 p.Arg108Ter Pathogenic/Likely pathogenic ★★ same condition
SPATA7 p.Arg391Ter Pathogenic/Likely pathogenic ★★ same condition
SPATA7 p.Arg395Ter Pathogenic/Likely pathogenic ★★ same condition
SPATA7 p.Arg85Ter Pathogenic/Likely pathogenic ★★ same condition
SPATA7 p.Cys96Ter Pathogenic/Likely pathogenic ★★ same condition
SPATA7 p.Lys163Ter Pathogenic ★★ same condition
SPATA7 c.1028+5A>G Uncertain significance ★★ 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/spata7-p-ser210 (accessed [today's date]).

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