Is HGF p.Val3= (c.9G>A) pathogenic?

HGF p.Val3= (c.9G>A) is classified Likely benign in HGF (ClinVar, Single submitter, 1 submitter; last evaluated 2021-05-02). Very rare (popmax 0.00482%, eas).

How common is HGF p.Val3= (c.9G>A) in the general population?

HGF p.Val3= (c.9G>A) is very rare (popmax 0.00482%, eas) (gnomAD).

HGF p.Val3=

c.9G>A · VCV4896426

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00482%, eas)

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 5.2	GERP 1.8, phastCons 1
Overall
CADD	14.44	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00482% East Asian · 2/41,466 alleles

Filtering AF 0.000799% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000299%

Overall 0.000129% 2/1,556,310 alleles · very rare exomes 2/1,404,070 · genomes 0/152,240 · joint denominator

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: HGF
Protein: p.Val3=
Coding: c.9G>A
MANE Select: NM_000601
Type: single nucleotide variant
Location: chr7:81769963 (GRCh38)
Gene constraint: LOEUF 0.471 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 83.76 · 36 PDB

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

Similar variants

HGF p.Val3Leu Uncertain significance ★ ⚠ same residue
HGF p.Ala432Val Uncertain significance ★★ ⚠ same type
HGF p.Ala661Thr Uncertain significance ★★ ⚠ same type
HGF p.Arg168Trp Uncertain significance ★★ ⚠ same type
HGF p.Arg220Gln Uncertain significance ★★ ⚠ same type
HGF p.Arg242Gln Uncertain significance ★★ ⚠ same type
HGF p.Arg242Trp Uncertain significance ★★ ⚠ same type
HGF p.Arg328His 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/hgf-p-val3 (accessed [today's date]).

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