Is CHST14 p.Pro12Ser (c.34C>T) pathogenic?

CHST14 p.Pro12Ser (c.34C>T) is classified Uncertain significance in CHST14 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-09). AlphaMissense: likely benign (0.0903); No allele count reported in gnomAD v4.1 (AN 1,450,598); Associated with Cardiovascular phenotype.

What condition is associated with CHST14 p.Pro12Ser (c.34C>T)?

CHST14 p.Pro12Ser (c.34C>T) is associated with Cardiovascular phenotype (ClinVar).

How common is CHST14 p.Pro12Ser (c.34C>T) in the general population?

CHST14 p.Pro12Ser (c.34C>T) is no allele count reported in gnomAD v4.1 (AN 1,450,598) (gnomAD).

What do computational predictors say about CHST14 p.Pro12Ser (c.34C>T)?

AlphaMissense predicts likely benign (score 0.0903) — an in-silico prediction, not a clinical call.

CHST14 p.Pro12Ser

c.34C>T · rs2543005170 · VCV1732048

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0903 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,450,598)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.0903	likely benign
REVEL	0.084	moderately benign-leaning
SaProt	LLR -6.91	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.9	GERP -2, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 1,127 bp · p 0.038 · regional, not allelic
Overall
CADD	16.56	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,450,598). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CHST14
Protein: p.Pro12Ser
Coding: c.34C>T
MANE Select: NM_130468
dbSNP: rs2543005170
Type: single nucleotide variant
Location: chr15:40471247 (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-pro12ser (accessed [today's date]).

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