Is TTC19 c.230C>T pathogenic?

TTC19 c.230C>T is classified Likely benign in TTC19 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-11-09). Very rare (popmax 0.00355%, sas); Associated with Inborn genetic diseases.

What condition is associated with TTC19 c.230C>T?

TTC19 c.230C>T is associated with Inborn genetic diseases (ClinVar).

How common is TTC19 c.230C>T in the general population?

TTC19 c.230C>T is very rare (popmax 0.00355%, sas) (gnomAD).

TTC19 c.230C>T

rs2549917409 · VCV2259967

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00355%, sas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.012	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.8	GERP -2.7
Non-coding constraint	Z 3.07	1 kb window · o/e 0.79 · regional · uncalibrated
Overall
CADD	1.99	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00355% South Asian · 3/84,466 alleles

Filtering AF 0.000943% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000462%

Overall 0.000388% 6/1,545,368 alleles · very rare exomes 6/1,393,008 · genomes 0/152,360 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00355%	28,155
African / African-American	0.00273%	36,685
European (non-Finnish)	8.75e-05%	1,142,589

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.230C>T
MANE Select: NM_017775
dbSNP: rs2549917409
Type: single nucleotide variant
Location: chr17:15999715 (GRCh38)
Gene constraint: LOEUF 1.049 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.28

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

Similar variants

TTC19 p.Ala200Val Uncertain significance ★★ ⚠ same condition
TTC19 p.Ala263Ser Uncertain significance ★★ ⚠ same condition
TTC19 p.Ala85Val Uncertain significance ★★ ⚠ same condition
TTC19 p.Arg102Gly Uncertain significance ★★ ⚠ same condition
TTC19 p.Arg124His Uncertain significance ★★ ⚠ same condition
TTC19 p.Arg294Cys Uncertain significance ★★ ⚠ same condition
TTC19 p.Ile206Met Uncertain significance ★★ ⚠ same condition
TTC19 p.Lys160Gln 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/ttc19-c-230c-t (accessed [today's date]).

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