Is IVD p.Pro291= (c.873T>C) pathogenic?

IVD p.Pro291= (c.873T>C) is classified Likely benign in IVD (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-26). Ultra-rare (popmax 0.0107%, afr); Associated with isovaleric acidemia.

What condition is associated with IVD p.Pro291= (c.873T>C)?

IVD p.Pro291= (c.873T>C) is associated with isovaleric acidemia (ClinVar).

How common is IVD p.Pro291= (c.873T>C) in the general population?

IVD p.Pro291= (c.873T>C) is ultra-rare (popmax 0.0107%, afr) (gnomAD).

How is Isovaleric acidemia inherited?

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

IVD p.Pro291=

c.873T>C · rs537402391 · VCV1602506

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0107%, afr)

Conditions

isovaleric acidemia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.038	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.36	GERP -3.5, phastCons 0.078
Overall
CADD	8.16	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0107% African / African-American · 8/75,066 alleles

Filtering AF 0.00527% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0038%

Overall 0.000558% 9/1,613,696 alleles · ultra-rare exomes 5/1,461,398 · genomes 4/152,298 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0107%	9,383
European (non-Finnish)	8.48e-05%	1,179,908

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: IVD
Protein: p.Pro291=
Coding: c.873T>C
MANE Select: NM_002225
dbSNP: rs537402391
Type: single nucleotide variant
Location: chr15:40414977 (GRCh38)
Gene constraint: LOEUF 0.776 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.25 · 5 PDB
Residue 291: a UniProt-annotated variant site (in iva; uncertain significance)

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

Disease context

isovaleric acidemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Isovaleric acidemia (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Childhood, Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

IVD p.Pro291Leu Likely pathogenic ★ same residue
IVD p.Pro291Ala Uncertain significance ★ ⚠ same residue
IVD p.Pro291fs Pathogenic ★★ same residue
IVD c.144+1G>A Likely pathogenic ★★ same condition
IVD c.144+1G>C Pathogenic ★★ same condition
IVD c.286+2T>C Pathogenic/Likely pathogenic ★★ same condition
IVD c.286+5G>T Likely pathogenic ★★ same condition
IVD c.287-1G>A 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/ivd-p-pro291 (accessed [today's date]).

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