Is TTC19 c.145C>A pathogenic?

TTC19 c.145C>A is classified Uncertain significance in TTC19 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-11-30). Very rare (popmax 0.000173%, nfe); Associated with Inborn genetic diseases.

What condition is associated with TTC19 c.145C>A?

TTC19 c.145C>A is associated with Inborn genetic diseases (ClinVar).

How common is TTC19 c.145C>A in the general population?

TTC19 c.145C>A is very rare (popmax 0.000173%, nfe) (gnomAD).

TTC19 c.145C>A

rs1451865654 · VCV2262587

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000173%, nfe)

Conditions

Inborn genetic diseases

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.024	moderately benign-leaning
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -1.5	GERP -3
Non-coding constraint	Z 3.07	1 kb window · o/e 0.79 · regional · uncalibrated
Overall
CADD	1.453	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000173% European (non-Finnish) · 2/1,156,992 alleles

Filtering AF 2.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000128% 2/1,566,444 alleles · very rare exomes 2/1,414,122 · genomes 0/152,322 · 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: TTC19
Coding: c.145C>A
MANE Select: NM_017775
dbSNP: rs1451865654
Type: single nucleotide variant
Location: chr17:15999630 (GRCh38)

Full TTC19 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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/ttc19-c-145c-a (accessed [today's date]).

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