Is CFP p.Val30Met (c.88G>A) pathogenic?

CFP p.Val30Met (c.88G>A) is classified Benign/Likely benign in CFP (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-11). AlphaMissense: likely benign (0.2761); Rare (popmax 0.265%, mid).

How common is CFP p.Val30Met (c.88G>A) in the general population?

CFP p.Val30Met (c.88G>A) is rare (popmax 0.265%, mid) (gnomAD).

What do computational predictors say about CFP p.Val30Met (c.88G>A)?

AlphaMissense predicts likely benign (score 0.2761) — an in-silico prediction, not a clinical call.

CFP p.Val30Met

c.88G>A · rs138456565 · VCV1543780

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.2761 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.265%, mid)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2761	likely benign
REVEL	0.256	benign-leaning
SaProt	LLR -10.09	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.7	GERP 1.6, phastCons 0.99
Regional constraint	o/e 0.79	unconstrained · MANE · 5,566 bp · p 3.9e-05 · regional, not allelic
Overall
CADD	20.6	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 0.265% Middle Eastern · 6/2,265 alleles

Filtering AF 0.115% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0788%

Overall 0.0327% 170/520,037 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.265%	377
South Asian	0.0557%	1,794
European (non-Finnish)	0.0372%	2,688
Remaining individualsnot grpmax-eligible	0.0325%	3,081
Admixed American	0.0193%	5,185
Finnishnot grpmax-eligible	0.00776%	12,892
African / African-American	0.00261%	38,385

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: CFP
Protein: p.Val30Met
Coding: c.88G>A
MANE Select: NM_001145252
dbSNP: rs138456565
Type: single nucleotide variant
Location: chrX:47629663 (GRCh38)
Structure: AlphaFold pLDDT 83.75 · 14 PDB
Residue 30: the tsp type-1 0 domain; a β-strand

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

Similar variants

CFP p.Trp321Gly Pathogenic ★★ same type
CFP p.Ala402Gly Uncertain significance ★★ ⚠ same type
CFP p.Arg157Gln Uncertain significance ★★ ⚠ same type
CFP p.Arg157Trp Uncertain significance ★★ ⚠ same type
CFP p.Arg159Cys Uncertain significance ★★ ⚠ same type
CFP p.Arg247Trp Uncertain significance ★★ ⚠ same type
CFP p.Arg438Trp Uncertain significance ★★ ⚠ same type
CFP p.Asn307Ser 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/cfp-p-val30met (accessed [today's date]).

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