Is HTRA2 p.Val109= (c.327G>A) pathogenic?

HTRA2 p.Val109= (c.327G>A) is classified Likely benign in HTRA2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-09). Ultra-rare (popmax 0.0331%, mid).

How common is HTRA2 p.Val109= (c.327G>A) in the general population?

HTRA2 p.Val109= (c.327G>A) is ultra-rare (popmax 0.0331%, mid) (gnomAD).

HTRA2 p.Val109=

c.327G>A · rs767562490 · VCV1597092

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0331%, mid)

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 0.91	GERP 0.61, phastCons 1
Overall
CADD	12.11	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0331% Middle Eastern · 2/6,034 alleles

Filtering AF 0.00584% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00305%

Overall 0.00358% 57/1,591,562 alleles · ultra-rare exomes 53/1,439,324 · genomes 4/152,238 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0331%	3,017
European (non-Finnish)	0.00437%	22,889
Admixed American	0.00346%	28,902
Remaining individualsnot grpmax-eligible	0.00327%	30,618

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: HTRA2
Protein: p.Val109=
Coding: c.327G>A
MANE Select: NM_013247
dbSNP: rs767562490
Type: single nucleotide variant
Location: chr2:74530333 (GRCh38)
Gene constraint: LOEUF 0.778 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.83 · 13 PDB

Full HTRA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

HTRA2 p.Arg380Ter Pathogenic ★★ same type
HTRA2 p.Gln82Ter Pathogenic ★★ same type
AUP1 p.Pro9Ser Uncertain significance ★★ ⚠ same type
HTRA2 c.507-10T>A Uncertain significance ★★ same type
HTRA2 c.507-9C>A Uncertain significance ★★ same type
HTRA2 p.Ala110Gly Uncertain significance ★★ ⚠ same type
HTRA2 p.Ala415Thr Uncertain significance ★★ ⚠ same type
HTRA2 p.Arg252Gln Uncertain significance ★★ ⚠ 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/htra2-p-val109 (accessed [today's date]).

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