Is FUCA1 p.Pro13Ala (c.37C>G) pathogenic?

FUCA1 p.Pro13Ala (c.37C>G) is classified Likely benign in FUCA1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-12). AlphaMissense: likely benign (0.0533); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with FUCA1 p.Pro13Ala (c.37C>G)?

FUCA1 p.Pro13Ala (c.37C>G) is associated with Inborn genetic diseases (ClinVar).

How common is FUCA1 p.Pro13Ala (c.37C>G) in the general population?

FUCA1 p.Pro13Ala (c.37C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about FUCA1 p.Pro13Ala (c.37C>G)?

AlphaMissense predicts likely benign (score 0.0533) — an in-silico prediction, not a clinical call.

FUCA1 p.Pro13Ala

c.37C>G · rs569701574 · VCV3097435

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0533 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0533	likely benign
REVEL	0.03	moderately benign-leaning
SaProt	LLR -5.90	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 -7.1	GERP -4.2
Regional constraint	o/e 0.96	unconstrained · MANE · 23 kb · p 0.31 · regional, not allelic
Overall
CADD	0.013	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

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: FUCA1
Protein: p.Pro13Ala
Coding: c.37C>G
MANE Select: NM_000147
dbSNP: rs569701574
Type: single nucleotide variant
Location: chr1:23868250 (GRCh38)
Gene constraint: LOEUF 1.162 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.60 · 2 PDB

Full FUCA1 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

FUCA1 p.Pro13Ser Uncertain significance ★★ ⚠ same residue
FUCA1 p.Pro13= Likely benign ★ same residue
FUCA1 p.Ala368Thr Uncertain significance ★★ ⚠ same condition
FUCA1 p.Arg162Gln Uncertain significance ★★ ⚠ same condition
FUCA1 p.Arg162Trp Uncertain significance ★★ ⚠ same condition
FUCA1 p.Arg173Gln Uncertain significance ★★ ⚠ same condition
FUCA1 p.Arg178His Uncertain significance ★★ ⚠ same condition
FUCA1 p.Arg30Trp 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/fuca1-p-pro13ala (accessed [today's date]).

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