Is CACNA1F p.Arg792Ser (c.2376G>T) pathogenic?

CACNA1F p.Arg792Ser (c.2376G>T) is classified Uncertain significance in CACNA1F (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-10). AlphaMissense: likely benign (0.0913); Absent from gnomAD v4.1.

How common is CACNA1F p.Arg792Ser (c.2376G>T) in the general population?

CACNA1F p.Arg792Ser (c.2376G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CACNA1F p.Arg792Ser (c.2376G>T)?

AlphaMissense predicts likely benign (score 0.0913) — an in-silico prediction, not a clinical call.

CACNA1F p.Arg792Ser

c.2376G>T · rs2147911088 · VCV1488353

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0913 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0913	likely benign
REVEL	0.043	moderately benign-leaning
SaProt	LLR -6.38	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.28	donor gain · deltas
Constraint at this position
Conservation	phyloP 2.7	GERP 0.51, phastCons 0.99
Regional constraint	o/e 0.84	unconstrained · MANE · 21 kb · p 1.1e-07 · regional, not allelic
Overall
CADD	10.13	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.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM R803S vs ClinVar R792S) — verify the residue.

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: CACNA1F
Protein: p.Arg792Ser
Coding: c.2376G>T
MANE Select: NM_001256789
dbSNP: rs2147911088
Type: single nucleotide variant
Location: chrX:49220483 (GRCh38)
Structure: AlphaFold pLDDT 67.46
Residue 792: the 'disordered' region

Full CACNA1F gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CACNA1F c.1118+1G>C Pathogenic ★★ same type
CACNA1F c.2086-1G>C Pathogenic/Likely pathogenic ★★ same type
CACNA1F c.2086-2A>G Pathogenic/Likely pathogenic ★★ same type
CACNA1F c.2543+1G>A Pathogenic ★★ same type
CACNA1F c.2674-2A>G Likely pathogenic ★★ same type
CACNA1F c.2928+1G>A Pathogenic ★★ same type
CACNA1F c.3236+1G>A Pathogenic/Likely pathogenic ★★ same type
CACNA1F c.381+1G>A Likely pathogenic ★★ 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/cacna1f-p-arg792ser (accessed [today's date]).

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