Is CTC1 p.Ser11= (c.33C>T) pathogenic?

CTC1 p.Ser11= (c.33C>T) is classified Uncertain significance in CTC1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2021-09-24). Ultra-rare (popmax 0.0232%, sas); Associated with cerebroretinal microangiopathy with calcifications and cysts 1.

How common is CTC1 p.Ser11= (c.33C>T) in the general population?

CTC1 p.Ser11= (c.33C>T) is ultra-rare (popmax 0.0232%, sas) (gnomAD).

How is Coats plus syndrome inherited?

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

CTC1 p.Ser11=

Q: What condition is associated with CTC1 p.Ser11= (c.33C>T)?

CTC1 p.Ser11= (c.33C>T) is associated with cerebroretinal microangiopathy with calcifications and cysts 1, dyskeratosis congenita (ClinVar).

c.33C>T · rs757066174 · VCV326090

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0232%, sas)

Conditions

cerebroretinal microangiopathy with calcifications and cysts 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.84	GERP -4.7
Overall
CADD	1.396	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0232% South Asian · 21/90,648 alleles

Filtering AF 0.0154% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.013%

Overall 0.00247% 36/1,458,522 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0232%	4,317
European (non-Finnish)	0.00127%	78,568

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: CTC1
Protein: p.Ser11=
Coding: c.33C>T
MANE Select: NM_012393 · reported on NM_025099
dbSNP: rs757066174
Type: single nucleotide variant
Location: chr17:8248004 (GRCh38)

Full CTC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

cerebroretinal microangiopathy with calcifications and cysts 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: dyskeratosis congenita

For Coats plus syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood
Prevalence: <1 / 1 000 000 (Europe)

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/ctc1-p-ser11 (accessed [today's date]).

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