Is TRAPPC9 p.Val3Ile (c.7G>A) pathogenic?

TRAPPC9 p.Val3Ile (c.7G>A) is classified Benign/Likely benign in TRAPPC9 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-25). AlphaMissense: likely benign (0.0662); Low-frequency (popmax 1.69%, afr); Associated with Inborn genetic diseases.

What condition is associated with TRAPPC9 p.Val3Ile (c.7G>A)?

TRAPPC9 p.Val3Ile (c.7G>A) is associated with Inborn genetic diseases, intellectual disability, autosomal recessive 13 (ClinVar).

How common is TRAPPC9 p.Val3Ile (c.7G>A) in the general population?

TRAPPC9 p.Val3Ile (c.7G>A) is low-frequency (popmax 1.69%, afr) (gnomAD).

What do computational predictors say about TRAPPC9 p.Val3Ile (c.7G>A)?

AlphaMissense predicts likely benign (score 0.0662) — an in-silico prediction, not a clinical call.

TRAPPC9 p.Val3Ile

c.7G>A · rs76033442 · VCV588070

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.0662 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.69%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0662	likely benign
REVEL	0.046	moderately benign-leaning
SaProt	LLR -4.92	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.7	GERP -0.52, phastCons 0.99
Regional constraint	o/e 0.81	unconstrained · MANE · 160 kb · p 6.1e-08 · regional, not allelic
Overall
CADD	20.2	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.69% African / African-American · 1,269/75,024 alleles

Filtering AF 1.61% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.58%

Overall 0.11% 1,770/1,602,594 alleles · low-frequency exomes 1,073/1,450,308 · genomes 697/152,286 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.69%	59
South Asian	0.388%	258
Remaining individualsnot grpmax-eligible	0.112%	892
Middle Eastern	0.099%	1,010
Admixed American	0.06%	1,667
East Asian	0.00446%	22,445
European (non-Finnish)	0.00288%	34,704

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: TRAPPC9
Protein: p.Val3Ile
Coding: c.7G>A
MANE Select: NM_001160372
dbSNP: rs76033442
Type: single nucleotide variant
Location: chr8:140451367 (GRCh38)
Gene constraint: LOEUF 0.786 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.98

Full TRAPPC9 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

Also linked: intellectual disability, autosomal recessive 13

Similar variants

TRAPPC9 c.2700-2A>T Pathogenic/Likely pathogenic ★★ same condition
TRAPPC9 c.3279+1G>A Pathogenic/Likely pathogenic ★★ same condition
TRAPPC9 p.Arg377Ter Pathogenic ★★ same condition
TRAPPC9 p.Arg472Ter Pathogenic/Likely pathogenic ★★ same condition
TRAPPC9 p.Arg51Ter Pathogenic/Likely pathogenic ★★ same condition
TRAPPC9 p.Arg614Ter Pathogenic ★★ same condition
TRAPPC9 p.Arg831Ter Pathogenic ★★ same condition
TRAPPC9 p.Glu123Ter Pathogenic ★★ 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/trappc9-p-val3ile (accessed [today's date]).

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