Is CHM p.Ser453Ter (c.1358_1359delinsGA) pathogenic?

CHM p.Ser453Ter (c.13581359delinsGA) is classified Pathogenic in CHM (ClinVar, No assertion criteria, 1 submitter; last evaluated 1992-06-01). Absent from gnomAD; Associated with choroideremia.

What condition is associated with CHM p.Ser453Ter (c.1358_1359delinsGA)?

CHM p.Ser453Ter (c.1358_1359delinsGA) is associated with choroideremia (ClinVar).

How common is CHM p.Ser453Ter (c.1358_1359delinsGA) in the general population?

CHM p.Ser453Ter (c.1358_1359delinsGA) is absent from gnomAD (gnomAD).

How is Choroideremia inherited?

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

CHM p.Ser453Ter

c.1358_1359delinsGA · rs132630263 · VCV11148

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

choroideremia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 11 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4	GERP -0.5, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CHM
Protein: p.Ser453Ter
Coding: c.1358_1359delinsGA
MANE Select: NM_000390
dbSNP: rs132630263
Type: Indel
Location: chrX:85900700 (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 p.Ser453= Conflicting classifications of pathogenicity ★ same residue
CHM p.Ser453fs Pathogenic ★ same residue
CHM c.117-546_126delinsAA Pathogenic ★ same condition
CHM c.703-1_727delinsTTAGAT Pathogenic ★ same condition
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

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-ser453ter (accessed [today's date]).

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