Is CHAMP1 p.Val162Phe (c.484G>T) pathogenic?

CHAMP1 p.Val162Phe (c.484G>T) is classified Likely benign in CHAMP1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-11-01). AlphaMissense: likely benign (0.11); Very rare (popmax 0.00288%, nfe); Associated with Inborn genetic diseases.

What condition is associated with CHAMP1 p.Val162Phe (c.484G>T)?

CHAMP1 p.Val162Phe (c.484G>T) is associated with Inborn genetic diseases (ClinVar).

How common is CHAMP1 p.Val162Phe (c.484G>T) in the general population?

CHAMP1 p.Val162Phe (c.484G>T) is very rare (popmax 0.00288%, nfe) (gnomAD).

What do computational predictors say about CHAMP1 p.Val162Phe (c.484G>T)?

AlphaMissense predicts likely benign (score 0.11) — an in-silico prediction, not a clinical call.

CHAMP1 p.Val162Phe

c.484G>T · rs1007989539 · VCV2237265

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.11 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00288%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.11	likely benign
REVEL	0.033	moderately benign-leaning
SaProt	LLR -8.66	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 0.5	GERP -2.9, phastCons 0.001
Regional constraint	o/e 1.21	unconstrained · MANE · 1,781 bp · p 1.6e-08 · regional, not allelic
Overall
CADD	16.13	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 0.00288% European (non-Finnish) · 34/1,180,032 alleles

Filtering AF 0.00207% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00183%

Overall 0.00223% 36/1,613,922 alleles · very rare exomes 33/1,461,854 · genomes 3/152,068 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00288%	34,707
Remaining individualsnot grpmax-eligible	0.0016%	62,482
Finnishnot grpmax-eligible	0.00156%	63,994

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: CHAMP1
Protein: p.Val162Phe
Coding: c.484G>T
MANE Select: NM_032436
dbSNP: rs1007989539
Type: single nucleotide variant
Location: chr13:114324326 (GRCh38)
Gene constraint: LOEUF 0.16 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 48.04 · 4 PDB
Residue 162: the 'disordered' region

Full CHAMP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CHAMP1 p.Ala304Val Uncertain significance ★★ ⚠ same condition
CHAMP1 p.Glu195Gly Uncertain significance ★★ ⚠ same condition
CHAMP1 p.Glu668Gln Uncertain significance ★★ ⚠ same condition
CHAMP1 p.Gly238Arg Uncertain significance ★★ ⚠ same condition
CHAMP1 p.Met671Thr Uncertain significance ★★ ⚠ same condition
CHAMP1 p.Pro150Leu Uncertain significance ★★ ⚠ same condition
CHAMP1 p.Pro265Ser Uncertain significance ★★ ⚠ same condition
CHAMP1 p.Pro477Ser Uncertain significance ★★ ⚠ same condition

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/champ1-p-val162phe (accessed [today's date]).

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