Is SOBP p.Ala764= (c.2292G>A) pathogenic?

SOBP p.Ala764= (c.2292G>A) is classified Likely benign in SOBP (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-11-16). Ultra-rare (popmax 0.0593%, sas); Associated with SOBP-related disorder.

What condition is associated with SOBP p.Ala764= (c.2292G>A)?

SOBP p.Ala764= (c.2292G>A) is associated with SOBP-related disorder (ClinVar).

How common is SOBP p.Ala764= (c.2292G>A) in the general population?

SOBP p.Ala764= (c.2292G>A) is ultra-rare (popmax 0.0593%, sas) (gnomAD).

SOBP p.Ala764=

c.2292G>A · rs571214895 · VCV3048361

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0593%, sas)

Conditions

SOBP-related disorder

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 -1	GERP 0.074
Overall
CADD	11.45	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0593% South Asian · 54/91,074 alleles

Filtering AF 0.0466% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0421%

Overall 0.00378% 61/1,613,118 alleles · ultra-rare exomes 55/1,460,994 · genomes 6/152,124 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0593%	1,687
Remaining individualsnot grpmax-eligible	0.00961%	10,408
European (non-Finnish)	8.48e-05%	1,179,746

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.Ala764=
Coding: c.2292G>A
MANE Select: NM_018013
dbSNP: rs571214895
Type: single nucleotide variant
Location: chr6:107635136 (GRCh38)
Gene constraint: LOEUF 0.191 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 52.41
Residue 764: the 'disordered' region

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

Disease context

SOBP-related disorder

Similar variants

SOBP p.Ala764Val Uncertain significance ★ ⚠ same residue
SOBP p.Pro763= Likely benign same condition
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

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-ala764 (accessed [today's date]).

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