Is ABAT p.Pro104Ala (c.310C>G) pathogenic?

ABAT p.Pro104Ala (c.310C>G) is classified Uncertain significance in ABAT (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-02). AlphaMissense: likely benign (0.3164); Ultra-rare (popmax 0.0176%, sas); Associated with Inborn genetic diseases.

What condition is associated with ABAT p.Pro104Ala (c.310C>G)?

ABAT p.Pro104Ala (c.310C>G) is associated with Inborn genetic diseases (ClinVar).

How common is ABAT p.Pro104Ala (c.310C>G) in the general population?

ABAT p.Pro104Ala (c.310C>G) is ultra-rare (popmax 0.0176%, sas) (gnomAD).

What do computational predictors say about ABAT p.Pro104Ala (c.310C>G)?

AlphaMissense predicts likely benign (score 0.3164) — an in-silico prediction, not a clinical call.

ABAT p.Pro104Ala

c.310C>G · VCV4231573

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3164 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0176%, sas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3164	likely benign
REVEL	0.639	indeterminate
SaProt	LLR -9.32	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2.1, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 46 kb · p 0.32 · regional, not allelic
Overall
CADD	26.6	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

Grpmax group 0.0176% South Asian · 16/91,046 alleles

Filtering AF 0.011% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00889%

Overall 0.00137% 20/1,460,756 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0176%	5,690
Remaining individualsnot grpmax-eligible	0.0048%	20,822
European (non-Finnish)	8.48e-05%	1,179,080

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.Pro104Ala
Coding: c.310C>G
MANE Select: NM_020686
Type: single nucleotide variant
Location: chr16:8750533 (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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

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ABAT p.Arg19Ser Uncertain significance ★★ ⚠ same condition
ABAT p.Arg313Thr Uncertain significance ★★ ⚠ same condition
ABAT p.Arg317Lys Uncertain significance ★★ ⚠ same condition
ABAT p.Arg401Gln Uncertain significance ★★ ⚠ same condition
ABAT p.Arg9Cys Uncertain significance ★★ ⚠ same condition

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-pro104ala (accessed [today's date]).

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