Is ASAH2 p.Ser79Phe (c.236C>T) pathogenic?

ASAH2 p.Ser79Phe (c.236C>T) is classified Uncertain significance in ASAH2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-29). AlphaMissense: likely benign (0.1073); Absent from gnomAD v4.1.

How common is ASAH2 p.Ser79Phe (c.236C>T) in the general population?

ASAH2 p.Ser79Phe (c.236C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ASAH2 p.Ser79Phe (c.236C>T)?

AlphaMissense predicts likely benign (score 0.1073) — an in-silico prediction, not a clinical call.

ASAH2 p.Ser79Phe

c.236C>T · rs2540641867 · VCV2257825

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1073 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1073	likely benign
REVEL	0.081	moderately benign-leaning
SaProt	LLR -9.87	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.6	GERP -0.74, phastCons 0.048
Regional constraint	o/e 1.00	unconstrained · MANE · 50 kb · p 0.89 · regional, not allelic
Overall
CADD	16.66	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ASAH2
Protein: p.Ser79Phe
Coding: c.236C>T
MANE Select: NM_019893
dbSNP: rs2540641867
Type: single nucleotide variant
Location: chr10:50245346 (GRCh38)
Gene constraint: LOEUF 0.838 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.24 · 1 PDB
Residue 79: the 'disordered' region

Full ASAH2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ASAH2 p.Ala109Thr Uncertain significance ★ ⚠ same type
ASAH2 p.Ala22Thr Uncertain significance ★ ⚠ same type
ASAH2 p.Ala69Thr Uncertain significance ★ ⚠ same type
ASAH2 p.Arg108Gln Uncertain significance ★ ⚠ same type
ASAH2 p.Arg140Cys Uncertain significance ★ ⚠ same type
ASAH2 p.Arg140Gly Uncertain significance ★ ⚠ same type
ASAH2 p.Arg140His Uncertain significance ★ ⚠ same type
ASAH2 p.Arg152Gln 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/asah2-p-ser79phe (accessed [today's date]).

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