Is ASAP1 p.Gln263= (c.789G>A) pathogenic?

ASAP1 p.Gln263= (c.789G>A) is classified Benign in ASAP1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-05-24). Common (popmax 5.23%, afr) — too common for a highly-penetrant pathogenic allele.

ASAP1 p.Gln263=

Q: How common is ASAP1 p.Gln263= (c.789G>A) in the general population?

ASAP1 p.Gln263= (c.789G>A) is common (popmax 5.23%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.789G>A · rs113163415 · VCV769345

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 5.23%, afr) — too common for a highly-penetrant pathogenic allele

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.032	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.49	GERP -4.3, phastCons 0.029
Overall
CADD	6.407	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 5.23% African / African-American · 3,819/73,080 alleles

Filtering AF 5.09% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.03%

Overall 0.303% 4,770/1,574,346 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	5.23%	19
Middle Eastern	0.831%	120
Admixed American	0.55%	182
Remaining individualsnot grpmax-eligible	0.398%	251
European (non-Finnish)	0.0304%	3,289
Ashkenazi Jewishnot grpmax-eligible	0.0282%	3,544
South Asian	0.0193%	5,182

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: ASAP1
Protein: p.Gln263=
Coding: c.789G>A
MANE Select: NM_018482
dbSNP: rs113163415
Type: single nucleotide variant
Location: chr8:130169025 (GRCh38)
Gene constraint: LOEUF 0.439 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 72.05 · 5 PDB

Full ASAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ASAP1 p.Ala1035Gly Uncertain significance ★ ⚠ same type
ASAP1 p.Ala429Val Uncertain significance ★ ⚠ same type
ASAP1 p.Ala914Gly Uncertain significance ★ ⚠ same type
ASAP1 p.Arg212His Uncertain significance ★ ⚠ same type
ASAP1 p.Arg447Gln Uncertain significance ★ ⚠ same type
ASAP1 p.Arg710Ter Uncertain significance ★ same type
ASAP1 p.Arg764Gln Uncertain significance ★ ⚠ same type
ASAP1 p.Asn134Tyr 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/asap1-p-gln263 (accessed [today's date]).

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