Is TIMCC p.Gly68= (c.204G>A) pathogenic?

TIMCC p.Gly68= (c.204G>A) is classified Likely benign in TIMCC (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-05). Very rare (popmax 0.00663%, nfe).

How common is TIMCC p.Gly68= (c.204G>A) in the general population?

TIMCC p.Gly68= (c.204G>A) is very rare (popmax 0.00663%, nfe) (gnomAD).

TIMCC p.Gly68=

c.204G>A · VCV4955469

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00663%, nfe)

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 -0.35	GERP -0.87
Overall
CADD	5.476	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00663% European (non-Finnish) · 76/1,145,774 alleles

Filtering AF 0.00543% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00496%

Overall 0.00543% 84/1,548,288 alleles · very rare exomes 76/1,396,016 · genomes 8/152,272 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00663%	15,076
African / African-American	0.00411%	24,340
South Asian	0.00358%	27,931
Remaining individualsnot grpmax-eligible	0.00334%	29,982

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: TIMCC
Protein: p.Gly68=
Coding: c.204G>A
MANE Select: NM_001329752
Type: single nucleotide variant
Location: chr2:70301808 (GRCh38)
Structure: AlphaFold pLDDT 95.42

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

Similar variants

TIMCC p.Asn24= Benign/Likely benign ★★ same type
FAM136A p.Gln183Ter Pathogenic ★ same type
FAM136A p.Ala12Val Uncertain significance ★ ⚠ same type
FAM136A p.Ala144Thr Uncertain significance ★ same type
FAM136A p.Ala203Asp Uncertain significance ★ ⚠ same type
FAM136A p.Ala2Val Uncertain significance ★ ⚠ same type
FAM136A p.Arg163Gly Uncertain significance ★ ⚠ same type
FAM136A p.Gln10His Uncertain significance ★ ⚠ same type

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/timcc-p-gly68 (accessed [today's date]).

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