Is ASCL4 p.Ala39Ser (c.115G>T) pathogenic?

ASCL4 p.Ala39Ser (c.115G>T) is classified Likely benign in ASCL4 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-03). Very rare (popmax 0.00334%, amr).

How common is ASCL4 p.Ala39Ser (c.115G>T) in the general population?

ASCL4 p.Ala39Ser (c.115G>T) is very rare (popmax 0.00334%, amr) (gnomAD).

ASCL4 p.Ala39Ser

c.115G>T · VCV3952122

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00334%, amr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.267	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.28	GERP -3.2
Regional constraint	o/e 1.28	unconstrained · MANE · 515 bp · p 5.2e-06 · regional, not allelic
Overall
CADD	2.671	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00334% Admixed American · 2/59,830 alleles

Filtering AF 0.000555% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000208%

Overall 0.000186% 3/1,609,420 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00334%	29,915
European (non-Finnish)	8.49e-05%	1,178,008

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: ASCL4
Protein: p.Ala39Ser
Coding: c.115G>T
MANE Select: NM_203436
Type: single nucleotide variant
Location: chr12:107775333 (GRCh38)
Gene constraint: LOEUF 1.921 · pLI 0.13 (gnomAD)
Structure: AlphaFold pLDDT 71.48

Full ASCL4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ASCL4 p.Ala141Thr Uncertain significance ★ same type
ASCL4 p.Ala157Ser Uncertain significance ★ same type
ASCL4 p.Ala160Val Uncertain significance ★ same type
ASCL4 p.Ala50Glu Uncertain significance ★ same type
ASCL4 p.Ala68Thr Uncertain significance ★ same type
ASCL4 p.Arg115Cys Uncertain significance ★ same type
ASCL4 p.Arg32Gln Uncertain significance ★ same type
ASCL4 p.Arg33Gly 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/ascl4-p-ala39ser (accessed [today's date]).

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