Is TRAPPC11 p.Arg225= (c.675G>A) pathogenic?

TRAPPC11 p.Arg225= (c.675G>A) is classified Benign in TRAPPC11 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-29). Common (popmax 5.24%, afr) — too common for a highly-penetrant pathogenic allele; Associated with autosomal recessive limb-girdle muscular dystrophy type R18.

What condition is associated with TRAPPC11 p.Arg225= (c.675G>A)?

TRAPPC11 p.Arg225= (c.675G>A) is associated with autosomal recessive limb-girdle muscular dystrophy type R18 (ClinVar).

TRAPPC11 p.Arg225=

Q: How common is TRAPPC11 p.Arg225= (c.675G>A) in the general population?

TRAPPC11 p.Arg225= (c.675G>A) is common (popmax 5.24%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

Q: How is TRAPPC11-related limb-girdle muscular dystrophy R18 inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.675G>A · rs73872657 · VCV474367

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Common

common (popmax 5.24%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

autosomal recessive limb-girdle muscular dystrophy type R18

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 1.9	GERP -0.55, phastCons 1
Overall
CADD	7.02	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 5.24% African / African-American · 3,752/71,642 alleles

Filtering AF 5.1% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.04%

Overall 0.279% 4,216/1,512,986 alleles · common exomes 1,869/1,361,114 · genomes 2,347/151,872 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	5.24%	19
Admixed American	0.378%	264
Remaining individualsnot grpmax-eligible	0.33%	303
Middle Eastern	0.225%	444
South Asian	0.0113%	8,860
European (non-Finnish)	0.00594%	16,834

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: TRAPPC11
Protein: p.Arg225=
Coding: c.675G>A
MANE Select: NM_021942
dbSNP: rs73872657
Type: single nucleotide variant
Location: chr4:183675178 (GRCh38)
Gene constraint: LOEUF 0.816 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.76

Full TRAPPC11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

autosomal recessive limb-girdle muscular dystrophy type R18 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For TRAPPC11-related limb-girdle muscular dystrophy R18 (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy

Similar variants

TRAPPC11 c.1113+2T>G Likely pathogenic ★★ same condition
TRAPPC11 c.1287+5G>A Pathogenic/Likely pathogenic ★★ same condition
TRAPPC11 c.1366+1G>A Likely pathogenic ★★ same condition
TRAPPC11 c.1568-1G>T Pathogenic/Likely pathogenic ★★ same condition
TRAPPC11 p.Arg1065Ter Pathogenic ★★ same condition
TRAPPC11 p.Arg34Ter Pathogenic/Likely pathogenic ★★ same condition
TRAPPC11 p.Arg398Ter Pathogenic/Likely pathogenic ★★ same condition
TRAPPC11 p.Arg450Ter Pathogenic/Likely 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/trappc11-p-arg225 (accessed [today's date]).

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