Is SOX10 p.Pro48= (c.144A>C) pathogenic?

SOX10 p.Pro48= (c.144A>C) is classified Likely benign in SOX10 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-03-21). Very rare (popmax 0.00168%, amr).

How common is SOX10 p.Pro48= (c.144A>C) in the general population?

SOX10 p.Pro48= (c.144A>C) is very rare (popmax 0.00168%, amr) (gnomAD).

SOX10 p.Pro48=

c.144A>C · rs1601887003 · VCV680429

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00168%, amr)

⚠ 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 -3.5	GERP -3.6
Overall
CADD	1.161	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00168% Admixed American · 1/59,492 alleles

Overall 0.000125% 2/1,600,048 alleles · very rare exomes 2/1,447,914 · genomes 0/152,134 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00168%	59,492
European (non-Finnish)	8.49e-05%	1,177,498

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.Pro48=
Coding: c.144A>C
MANE Select: NM_006941
dbSNP: rs1601887003
Type: single nucleotide variant
Location: chr22:37983641 (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-pro48 (accessed [today's date]).

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