Is TTC19 c.*27G>A pathogenic?

TTC19 c.27G>A is classified Conflicting classifications of pathogenicity in TTC19 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2020-02-25). Rare (popmax 0.716%, sas); Associated with mitochondrial complex III deficiency nuclear type 2.

What condition is associated with TTC19 c.*27G>A?

TTC19 c.*27G>A is associated with mitochondrial complex III deficiency nuclear type 2 (ClinVar).

How common is TTC19 c.*27G>A in the general population?

TTC19 c.*27G>A is rare (popmax 0.716%, sas) (gnomAD).

TTC19 c.*27G>A

rs150843177 · VCV321951

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.716%, sas)

Conditions

mitochondrial complex III deficiency nuclear type 2

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 0.82	GERP 0.6, phastCons 0.001
Non-coding constraint	Z 1.49	1 kb window · o/e 0.89 · regional · uncalibrated
Overall
CADD	3.477	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.716% South Asian · 651/90,974 alleles

Filtering AF 0.67% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.652%

Overall 0.111% 1,788/1,612,068 alleles · rare exomes 1,661/1,459,880 · genomes 127/152,188 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.716%	140
European (non-Finnish)	0.0876%	1,142
Admixed American	0.08%	1,250
Remaining individualsnot grpmax-eligible	0.0689%	1,452
African / African-American	0.016%	6,248
Finnishnot grpmax-eligible	0.00314%	31,867

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.*27G>A
MANE Select: NM_017775
dbSNP: rs150843177
Type: single nucleotide variant
Location: chr17:16027549 (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

mitochondrial complex III deficiency nuclear type 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TTC19 p.Gln195Ter Pathogenic/Likely pathogenic ★★ same condition
TTC19 p.Leu185Pro Pathogenic/Likely pathogenic ★★ same condition
TTC19 p.Leu219Ter Pathogenic ★★ same condition
TTC19 c.581+4A>C Uncertain significance ★★ same condition
TTC19 c.994+3A>T Uncertain significance ★★ same condition
TTC19 p.Ala122Thr Uncertain significance ★★ ⚠ same condition
TTC19 p.Ala263Ser Uncertain significance ★★ ⚠ same condition
TTC19 p.Arg102Gly 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-star-27g-a (accessed [today's date]).

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