Is SOX10 p.Pro14= (c.42C>T) pathogenic?

SOX10 p.Pro14= (c.42C>T) is classified Likely benign in SOX10 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-08). Ultra-rare (popmax 0.0163%, sas).

How common is SOX10 p.Pro14= (c.42C>T) in the general population?

SOX10 p.Pro14= (c.42C>T) is ultra-rare (popmax 0.0163%, sas) (gnomAD).

SOX10 p.Pro14=

c.42C>T · VCV4947889

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0163%, sas)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -1.3	GERP -0.98
Overall
CADD	11.7	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0163% South Asian · 13/79,964 alleles

Filtering AF 0.00954% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00756%

Overall 0.00108% 16/1,484,230 alleles · ultra-rare exomes 14/1,332,720 · genomes 2/151,510 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0163%	6,151
Finnishnot grpmax-eligible	0.0046%	21,716
East Asian	0.00269%	37,240

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: SOX10
Protein: p.Pro14=
Coding: c.42C>T
MANE Select: NM_006941
Type: single nucleotide variant
Location: chr22:37983743 (GRCh38)

Full SOX10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/sox10-p-pro14 (accessed [today's date]).

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