Is SOX10 p.Pro241= (c.723T>A) pathogenic?

SOX10 p.Pro241= (c.723T>A) is classified Likely benign in SOX10 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2024-09-16). Rare (popmax 0.798%, eas).

How common is SOX10 p.Pro241= (c.723T>A) in the general population?

SOX10 p.Pro241= (c.723T>A) is rare (popmax 0.798%, eas) (gnomAD).

SOX10 p.Pro241=

c.723T>A · rs1601879433 · VCV759071

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

rare (popmax 0.798%, eas)

⚠ 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.
REVEL	0.082	moderately benign-leaning
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 2.8	GERP -0.56, phastCons 1
Overall
CADD	9.311	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.798% East Asian · 198/24,816 alleles

Filtering AF 0.707% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.672%

Overall 0.266% 2,900/1,092,018 alleles · rare exomes 2,865/948,288 · genomes 35/143,730 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.798%	125
Remaining individualsnot grpmax-eligible	0.542%	184
Ashkenazi Jewishnot grpmax-eligible	0.526%	190
Middle Eastern	0.498%	201
European (non-Finnish)	0.268%	373
African / African-American	0.205%	488
Admixed American	0.155%	646
Finnishnot grpmax-eligible	0.135%	739
South Asian	0.0544%	1,837

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.Pro241=
Coding: c.723T>A
MANE Select: NM_006941
dbSNP: rs1601879433
Type: single nucleotide variant
Location: chr22:37974173 (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-pro241 (accessed [today's date]).

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