Is CHST14 p.Arg62= (c.186G>T) pathogenic?

CHST14 p.Arg62= (c.186G>T) is classified Likely benign in CHST14 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-12). Very rare (popmax 8.65e-05%, nfe); Associated with Cardiovascular phenotype.

What condition is associated with CHST14 p.Arg62= (c.186G>T)?

CHST14 p.Arg62= (c.186G>T) is associated with Cardiovascular phenotype (ClinVar).

How common is CHST14 p.Arg62= (c.186G>T) in the general population?

CHST14 p.Arg62= (c.186G>T) is very rare (popmax 8.65e-05%, nfe) (gnomAD).

CHST14 p.Arg62=

c.186G>T · rs1055352198 · VCV2451986

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.65e-05%, nfe)

Conditions

Cardiovascular phenotype

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 1.2	GERP -2.3, phastCons 1
Overall
CADD	9.933	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.65e-05% European (non-Finnish) · 1/1,155,598 alleles

Overall 6.42e-05% 1/1,557,322 alleles · very rare exomes 1/1,405,090 · genomes 0/152,232 · 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: CHST14
Protein: p.Arg62=
Coding: c.186G>T
MANE Select: NM_130468
dbSNP: rs1055352198
Type: single nucleotide variant
Location: chr15:40471399 (GRCh38)
Gene constraint: LOEUF 0.917 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.17

Full CHST14 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CHST14 p.Arg320Ter Likely pathogenic ★★ same condition
CHST14 p.Ala100Thr Uncertain significance ★★ ⚠ same condition
CHST14 p.Ala15Pro Uncertain significance ★★ ⚠ same condition
CHST14 p.Ala346Pro Uncertain significance ★★ ⚠ same condition
CHST14 p.Ala373Ser Uncertain significance ★★ ⚠ same condition
CHST14 p.Ala373Val Uncertain significance ★★ ⚠ same condition
CHST14 p.Ala52Val Uncertain significance ★★ ⚠ same condition
CHST14 p.Arg109Trp Uncertain significance ★★ ⚠ 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/chst14-p-arg62 (accessed [today's date]).

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