Is ARMC1 p.Ser4Phe (c.11C>T) pathogenic?

ARMC1 p.Ser4Phe (c.11C>T) is classified Uncertain significance in ARMC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-20). AlphaMissense: likely benign (0.1368); Absent from gnomAD v4.1.

How common is ARMC1 p.Ser4Phe (c.11C>T) in the general population?

ARMC1 p.Ser4Phe (c.11C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ARMC1 p.Ser4Phe (c.11C>T)?

AlphaMissense predicts likely benign (score 0.1368) — an in-silico prediction, not a clinical call.

ARMC1 p.Ser4Phe

c.11C>T · VCV4643016

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1368 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1368	likely benign
REVEL	0.114	moderately benign-leaning
SaProt	LLR -8.65	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 9.6	phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 14 kb · p 0.083 · regional, not allelic
Overall
CADD	24.1	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: ARMC1
Protein: p.Ser4Phe
Coding: c.11C>T
MANE Select: NM_018120
Type: single nucleotide variant
Location: chr8:65627388 (GRCh38)
Gene constraint: LOEUF 0.885 · pLI 0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.47

Full ARMC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ARMC1 p.Ser4= Likely benign ★ same residue
ARMC1 p.Ala25Val Uncertain significance ★ ⚠ same type
ARMC1 p.Ala266Pro Uncertain significance ★ ⚠ same type
ARMC1 p.Ala26Val Uncertain significance ★ ⚠ same type
ARMC1 p.Ala273Thr Uncertain significance ★ ⚠ same type
ARMC1 p.Arg127Cys Uncertain significance ★ ⚠ same type
ARMC1 p.Arg127His Uncertain significance ★ ⚠ same type
ARMC1 p.Arg141Ser 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/armc1-p-ser4phe (accessed [today's date]).

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