Is SOBP p.Asp783= (c.2349C>T) pathogenic?

SOBP p.Asp783= (c.2349C>T) is classified Uncertain significance in SOBP (ClinVar, Single submitter, 1 submitter; last evaluated 2015-02-11). Rare (popmax 0.442%, sas).

How common is SOBP p.Asp783= (c.2349C>T) in the general population?

SOBP p.Asp783= (c.2349C>T) is rare (popmax 0.442%, sas) (gnomAD).

SOBP p.Asp783=

c.2349C>T · rs367899598 · VCV212282

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.442%, sas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.086	GERP -0.64, phastCons 0.86
Overall
CADD	13.79	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.442% South Asian · 403/91,084 alleles

Filtering AF 0.407% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.393%

Overall 0.0266% 429/1,613,806 alleles · rare exomes 394/1,461,694 · genomes 35/152,112 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.442%	226
Remaining individualsnot grpmax-eligible	0.0352%	2,841
Middle Eastern	0.0165%	6,062
African / African-American	0.00133%	75,000
European (non-Finnish)	0.00017%	589,971

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: SOBP
Protein: p.Asp783=
Coding: c.2349C>T
MANE Select: NM_018013
dbSNP: rs367899598
Type: single nucleotide variant
Location: chr6:107635193 (GRCh38)
Gene constraint: LOEUF 0.191 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 52.41

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

Similar variants

SOBP p.Asp783Glu Uncertain significance ★ ⚠ same residue
SOBP c.573+12G>A Uncertain significance ★★ same type
SOBP p.Ala208Thr Uncertain significance ★★ ⚠ same type
SOBP p.Ala702Val Uncertain significance ★★ ⚠ same type
SOBP p.Glu89Lys Uncertain significance ★★ ⚠ same type
SOBP p.Lys862Asn Uncertain significance ★★ ⚠ same type
SOBP p.Pro138Leu Uncertain significance ★★ same type
SOBP p.Pro139Ser 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/sobp-p-asp783 (accessed [today's date]).

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