Is VCP p.Pro729= (c.2187T>G) pathogenic?

VCP p.Pro729= (c.2187T>G) is classified Benign in VCP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-29). Rare (popmax 0.164%, sas); Associated with inclusion body myopathy with Paget disease of bone and frontotemporal dementia.

How common is VCP p.Pro729= (c.2187T>G) in the general population?

VCP p.Pro729= (c.2187T>G) is rare (popmax 0.164%, sas) (gnomAD).

VCP p.Pro729=

Q: What condition is associated with VCP p.Pro729= (c.2187T>G)?

VCP p.Pro729= (c.2187T>G) is associated with inclusion body myopathy with Paget disease of bone and frontotemporal dementia, frontotemporal dementia and/or amyotrophic lateral sclerosis 6 (ClinVar).

Q: How is Inclusion body myopathy with Paget disease of bone and frontotemporal dementia inherited?

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

c.2187T>G · VCV3763101

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.164%, sas)

Conditions

inclusion body myopathy with Paget disease of bone and frontotemporal dementia

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 0.28	GERP -2.1, phastCons 0.73
Overall
CADD	7.974	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.164% South Asian · 149/91,086 alleles

Filtering AF 0.142% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.134%

Overall 0.00943% 152/1,612,526 alleles · rare exomes 143/1,460,140 · genomes 9/152,386 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.164%	611
European (non-Finnish)	0.000254%	393,346

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: VCP
Protein: p.Pro729=
Coding: c.2187T>G
MANE Select: NM_007126
Type: single nucleotide variant
Location: chr9:35057504 (GRCh38)
Gene constraint: LOEUF 0.134 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 83.11 · 144 PDB
Residue 729: an α-helix

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

Disease context

inclusion body myopathy with Paget disease of bone and frontotemporal dementia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: frontotemporal dementia and/or amyotrophic lateral sclerosis 6

For Inclusion body myopathy with Paget disease of bone and frontotemporal dementia (Orphanet):

Inheritance: Autosomal dominant
Onset: Adult

Similar variants

VCP p.Arg155Cys Pathogenic/Likely pathogenic ★★ same condition
VCP p.Arg155Gly Pathogenic/Likely pathogenic ★★ same condition
VCP p.Arg155His Pathogenic ★★ ⚠ same condition
VCP p.Arg159Cys Pathogenic/Likely pathogenic ★★ same condition
VCP p.Arg159His Pathogenic ★★ same condition
VCP p.Arg191Gln Pathogenic/Likely pathogenic ★★ same condition
VCP p.Arg191Pro Pathogenic/Likely pathogenic ★★ same condition
VCP p.Arg256Gly 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/vcp-p-pro729 (accessed [today's date]).

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