Is CHST10 p.Pro104Ser (c.310C>T) pathogenic?

CHST10 p.Pro104Ser (c.310C>T) is classified Uncertain significance in CHST10 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-12). AlphaMissense: likely benign (0.0653); Very rare (popmax 0.00988%, sas).

How common is CHST10 p.Pro104Ser (c.310C>T) in the general population?

CHST10 p.Pro104Ser (c.310C>T) is very rare (popmax 0.00988%, sas) (gnomAD).

What do computational predictors say about CHST10 p.Pro104Ser (c.310C>T)?

AlphaMissense predicts likely benign (score 0.0653) — an in-silico prediction, not a clinical call.

CHST10 p.Pro104Ser

c.310C>T · rs756854215 · VCV2254139

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0653 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00988%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0653	likely benign
REVEL	0.078	moderately benign-leaning
SaProt	LLR -7.30	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 -0.34	GERP -0.27
Regional constraint	o/e 0.89	unconstrained · MANE · 13 kb · p 0.019 · regional, not allelic
Overall
CADD	4.038	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

Grpmax group 0.00988% South Asian · 9/91,088 alleles

Filtering AF 0.00514% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00375%

Overall 0.000619% 10/1,614,210 alleles · very rare exomes 9/1,461,882 · genomes 1/152,328 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00988%	10,121
European (non-Finnish)	8.47e-05%	1,180,025

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: CHST10
Protein: p.Pro104Ser
Coding: c.310C>T
MANE Select: NM_004854
dbSNP: rs756854215
Type: single nucleotide variant
Location: chr2:100398025 (GRCh38)
Gene constraint: LOEUF 0.936 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.29

Full CHST10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

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CHST10 p.Arg208Trp Uncertain significance ★ ⚠ same type
CHST10 p.Arg229Trp Uncertain significance ★ ⚠ same type
CHST10 p.Arg242Cys Uncertain significance ★ ⚠ same type
CHST10 p.Arg330Gln Uncertain significance ★ ⚠ same type
CHST10 p.Arg333Gln Uncertain significance ★ ⚠ same type
CHST10 p.Arg84Leu 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/chst10-p-pro104ser (accessed [today's date]).

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