Is HCN4 p.Pro202= (c.606G>A) pathogenic?

HCN4 p.Pro202= (c.606G>A) is classified Likely benign in HCN4 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-02-27). Very rare (popmax 0.00879%, sas); Associated with Brugada syndrome 8.

What condition is associated with HCN4 p.Pro202= (c.606G>A)?

HCN4 p.Pro202= (c.606G>A) is associated with Brugada syndrome 8 (ClinVar).

How common is HCN4 p.Pro202= (c.606G>A) in the general population?

HCN4 p.Pro202= (c.606G>A) is very rare (popmax 0.00879%, sas) (gnomAD).

How is Brugada syndrome inherited?

Typically Autosomal dominant, Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

HCN4 p.Pro202=

c.606G>A · rs749297696 · VCV2885099

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00879%, sas)

Conditions

Brugada syndrome 8

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 -3.9	GERP -2.8
Overall
CADD	0.379	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00879% South Asian · 8/91,044 alleles

Filtering AF 0.00437% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00312%

Overall 0.000995% 16/1,607,292 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00879%	11,381
Remaining individualsnot grpmax-eligible	0.00321%	31,172
European (non-Finnish)	0.000509%	196,632

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: HCN4
Protein: p.Pro202=
Coding: c.606G>A
MANE Select: NM_005477
dbSNP: rs749297696
Type: single nucleotide variant
Location: chr15:73367665 (GRCh38)
Gene constraint: LOEUF 0.571 · pLI 0.15 (gnomAD)
Structure: AlphaFold pLDDT 61.86 · 8 PDB

Full HCN4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Brugada syndrome 8 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Brugada syndrome (Orphanet):

Inheritance: Autosomal dominant, Not applicable
Onset: Adult, Childhood
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

HCN4 p.Pro202Thr Uncertain significance ★★ ⚠ same residue
HCN4 p.Pro202Arg Uncertain significance ★ ⚠ same residue
HCN4 p.Pro202Gln Uncertain significance ★ ⚠ same residue
HCN4 p.Pro202Leu Uncertain significance ★ ⚠ same residue
HCN4 c.2143+1G>A Likely pathogenic ★★ same condition
HCN4 p.Ala485Val Pathogenic/Likely pathogenic ★★ same condition
HCN4 p.Arg375Cys Pathogenic/Likely pathogenic ★★ same condition
HCN4 p.Gly480Ser 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/hcn4-p-pro202 (accessed [today's date]).

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