Is TRIOBP p.Asp656= (c.1968C>T) pathogenic?

TRIOBP p.Asp656= (c.1968C>T) is classified Likely benign in TRIOBP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-10). Very rare (popmax 0.00341%, nfe).

How common is TRIOBP p.Asp656= (c.1968C>T) in the general population?

TRIOBP p.Asp656= (c.1968C>T) is very rare (popmax 0.00341%, nfe) (gnomAD).

TRIOBP p.Asp656=

c.1968C>T · rs376169386 · VCV1637853

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00341%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -3.1	GERP -2.4
Overall
CADD	6.324	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00341% European (non-Finnish) · 40/1,173,656 alleles

Filtering AF 0.00257% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00226%

Overall 0.00331% 53/1,601,556 alleles · very rare exomes 49/1,452,714 · genomes 4/148,842 · joint denominator

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.00806%	12,402
Finnishnot grpmax-eligible	0.00789%	12,679
European (non-Finnish)grpmax	0.00341%	29,341
Admixed American	0.00168%	59,378
African / African-American	0.00136%	73,322
South Asian	0.00112%	89,134

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: TRIOBP
Protein: p.Asp656=
Coding: c.1968C>T
MANE Select: NM_001039141
dbSNP: rs376169386
Type: single nucleotide variant
Location: chr22:37724524 (GRCh38)
Gene constraint: LOEUF 0.865 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 40.77
Residue 656: the 'disordered' region

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

Similar variants

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TRIOBP p.Arg1068Ter Pathogenic/Likely pathogenic ★★ same type
TRIOBP p.Arg1117Ter Pathogenic ★★ same type
TRIOBP p.Arg1745Ter Likely pathogenic ★★ same type
TRIOBP p.Arg347Ter Pathogenic ★★ same type
TRIOBP p.Arg399Ter Pathogenic/Likely pathogenic ★★ same type
TRIOBP p.Arg448Ter Pathogenic ★★ 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/triobp-p-asp656 (accessed [today's date]).

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