Is ABAT p.Ser3Tyr (c.8C>A) pathogenic?

ABAT p.Ser3Tyr (c.8C>A) is classified Uncertain significance in ABAT (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-29). AlphaMissense: likely benign (0.136); Very rare (popmax 0.0017%, amr).

How common is ABAT p.Ser3Tyr (c.8C>A) in the general population?

ABAT p.Ser3Tyr (c.8C>A) is very rare (popmax 0.0017%, amr) (gnomAD).

What do computational predictors say about ABAT p.Ser3Tyr (c.8C>A)?

AlphaMissense predicts likely benign (score 0.136) — an in-silico prediction, not a clinical call.

ABAT p.Ser3Tyr

c.8C>A · rs762912862 · VCV2507288

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.136 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0017%, amr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.136	likely benign
REVEL	0.173	moderately benign-leaning
SaProt	LLR -10.46	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.78	GERP -1.7, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 46 kb · p 0.32 · regional, not allelic
Overall
CADD	17.58	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0017% Admixed American · 1/58,870 alleles

Overall 6.88e-05% 1/1,452,550 alleles · very rare

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: ABAT
Protein: p.Ser3Tyr
Coding: c.8C>A
MANE Select: NM_020686
dbSNP: rs762912862
Type: single nucleotide variant
Location: chr16:8735747 (GRCh38)
Gene constraint: LOEUF 0.871 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 93.91

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

Similar variants

ABAT c.168+1G>A Pathogenic ★★ same type
ABAT p.Arg92Gln Pathogenic/Likely pathogenic ★★ ⚠ same type
ABAT p.Gln8Ter Pathogenic/Likely pathogenic ★★ same type
ABAT p.Leu211Phe Pathogenic/Likely pathogenic ★★ same type
ABAT p.Tyr376Ter Pathogenic/Likely pathogenic ★★ same type
ABAT c.1381+6G>T Uncertain significance ★★ same type
ABAT p.Ala162Thr Uncertain significance ★★ ⚠ same type
ABAT p.Ala226Val 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/abat-p-ser3tyr (accessed [today's date]).

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