Is CHM p.Gln540= (c.1620A>G) pathogenic?

CHM p.Gln540= (c.1620A>G) is classified Benign/Likely benign in CHM (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-10-03). Rare (popmax 0.164%, afr); Associated with choroideremia.

What condition is associated with CHM p.Gln540= (c.1620A>G)?

CHM p.Gln540= (c.1620A>G) is associated with choroideremia (ClinVar).

How common is CHM p.Gln540= (c.1620A>G) in the general population?

CHM p.Gln540= (c.1620A>G) is rare (popmax 0.164%, afr) (gnomAD).

How is Choroideremia inherited?

Typically X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

CHM p.Gln540=

c.1620A>G · rs140479582 · VCV1165868

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.164%, afr)

Conditions

choroideremia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.41	GERP -3.6, phastCons 0.001
Overall
CADD	1.05	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.164% African / African-American · 92/56,037 alleles

Filtering AF 0.137% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.127%

Overall 0.0112% 130/1,164,172 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.164%	609
Remaining individualsnot grpmax-eligible	0.0545%	1,836
Middle Eastern	0.0236%	4,237
Admixed American	0.018%	5,550
South Asian	0.00567%	17,624
European (non-Finnish)	0.000116%	860,230

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: CHM
Protein: p.Gln540=
Coding: c.1620A>G
MANE Select: NM_000390
dbSNP: rs140479582
Type: single nucleotide variant
Location: chrX:85873202 (GRCh38)
Structure: AlphaFold pLDDT 81.05

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

Disease context

choroideremia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Choroideremia (Orphanet):

Inheritance: X-linked recessive
Onset: Adolescent, Adult, Childhood
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

CHM c.116+1G>A Pathogenic/Likely pathogenic ★★ same condition
CHM c.116+1G>T Pathogenic/Likely pathogenic ★★ same condition
CHM c.1166+1G>A Pathogenic ★★ same condition
CHM c.1166+1G>C Pathogenic ★★ same condition
CHM c.1350-1G>A Pathogenic/Likely pathogenic ★★ same condition
CHM c.1413+1G>T Pathogenic ★★ same condition
CHM c.1511-1G>A Pathogenic ★★ same condition
CHM c.1511-2A>T Likely pathogenic ★★ 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/chm-p-gln540 (accessed [today's date]).

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