Is FUT5 p.Ser174Arg (c.520A>C) pathogenic?

FUT5 p.Ser174Arg (c.520A>C) is classified Likely benign in FUT5 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-21). AlphaMissense: likely benign (0.1452); Very rare (popmax 0.00896%, eas).

How common is FUT5 p.Ser174Arg (c.520A>C) in the general population?

FUT5 p.Ser174Arg (c.520A>C) is very rare (popmax 0.00896%, eas) (gnomAD).

What do computational predictors say about FUT5 p.Ser174Arg (c.520A>C)?

AlphaMissense predicts likely benign (score 0.1452) — an in-silico prediction, not a clinical call.

FUT5 p.Ser174Arg

c.520A>C · rs767078141 · VCV3097507

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1452 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00896%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1452	likely benign
REVEL	0.022	moderately benign-leaning
SaProt	LLR -4.40	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 -0.82	GERP -3.4
Regional constraint	o/e 1.08	unconstrained · MANE · 519 bp · p 0.24 · regional, not allelic
Overall
CADD	4.378	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 0.00896% East Asian · 4/44,648 alleles

Filtering AF 0.00299% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00181%

Overall 0.000274% 4/1,460,838 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: FUT5
Protein: p.Ser174Arg
Coding: c.520A>C
MANE Select: NM_002034
dbSNP: rs767078141
Type: single nucleotide variant
Location: chr19:5867206 (GRCh38)
Gene constraint: LOEUF 1.814 · pLI 0.11 (gnomAD)
Structure: AlphaFold pLDDT 88.70

Full FUT5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

FUT5 p.His334Arg Benign ★★ same type
FUT5 p.Thr338Met Benign ★★ ⚠ same type
FUT5 p.Ala101Gly Uncertain significance ★ ⚠ same type
FUT5 p.Ala101Val Uncertain significance ★ ⚠ same type
FUT5 p.Ala228Val Uncertain significance ★ ⚠ same type
FUT5 p.Ala277Ser Uncertain significance ★ ⚠ same type
FUT5 p.Ala277Thr Uncertain significance ★ ⚠ same type
FUT5 p.Ala277Val 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/fut5-p-ser174arg (accessed [today's date]).

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