Is CFC1 p.Arg78Trp (c.232C>T) pathogenic?

CFC1 p.Arg78Trp (c.232C>T) is classified Likely benign in CFC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2015-03-03). AlphaMissense: likely benign (0.1177); Absent from gnomAD v4.1.

How common is CFC1 p.Arg78Trp (c.232C>T) in the general population?

CFC1 p.Arg78Trp (c.232C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CFC1 p.Arg78Trp (c.232C>T)?

AlphaMissense predicts likely benign (score 0.1177) — an in-silico prediction, not a clinical call.

CFC1 p.Arg78Trp

c.232C>T · rs1318519716 · VCV1216095

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1177 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.1177	likely benign
REVEL	0.506	indeterminate
SaProt	LLR -7.57	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 -6.9
Regional constraint	o/e 0.12	constrained · MANE · 6,407 bp · p 3.7e-22 · regional, not allelic
Overall
CADD	0.374	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: CFC1
Protein: p.Arg78Trp
Coding: c.232C>T
MANE Select: NM_032545
dbSNP: rs1318519716
Type: single nucleotide variant
Location: chr2:130598657 (GRCh38)
Gene constraint: LOEUF 0.586 · pLI 0.86 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 64.18
Residue 78: a UniProt-annotated variant site (in)

Full CFC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFC1 p.Gly33Ser Uncertain significance ★★ ⚠ same type
CFC1 p.Ala145Thr Benign ★★ same type
CFC1 p.Arg47Gln Benign ★★ same type
CFC1 p.Asn21= Benign/Likely benign ★★ same type
CFC1 p.Asn21His Benign ★★ same type
CFC1 p.Gly59Arg Likely benign ★★ same type
CFC1 p.Leu202= Benign/Likely benign ★★ same type
CFC1 p.Ala195Val 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/cfc1-p-arg78trp (accessed [today's date]).

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