Is CHM p.Gln405Ter (c.1213C>T) pathogenic?

CHM p.Gln405Ter (c.1213C>T) is classified Pathogenic in CHM (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-11-05). Absent from gnomAD v4.1; Associated with inherited retinal dystrophy.

What condition is associated with CHM p.Gln405Ter (c.1213C>T)?

CHM p.Gln405Ter (c.1213C>T) is associated with inherited retinal dystrophy (ClinVar).

How common is CHM p.Gln405Ter (c.1213C>T) in the general population?

CHM p.Gln405Ter (c.1213C>T) is absent from gnomAD v4.1 (gnomAD).

CHM p.Gln405Ter

c.1213C>T · rs1057517715 · VCV372322

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,041,515)

Conditions

inherited retinal dystrophy

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 9 of 15
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.7	GERP 0.13, phastCons 1
Overall
CADD	36.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,041,515). 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.Gln405Ter
Coding: c.1213C>T
MANE Select: NM_000390
dbSNP: rs1057517715
Type: single nucleotide variant
Location: chrX:85911292 (GRCh38)
Structure: AlphaFold pLDDT 81.05

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

Disease context

inherited retinal dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CHM p.Gln405= Likely benign ★ same residue
CHM c.116+1G>A Pathogenic/Likely pathogenic ★★ same condition
CHM c.1244+1G>A Pathogenic ★★ same condition
CHM c.189+1G>A Pathogenic ★★ same condition
CHM c.49+5G>A Pathogenic/Likely pathogenic ★★ same condition
CHM c.940+1G>A Pathogenic ★★ same condition
CHM p.Arg239Ter Pathogenic ★★ same condition
CHM p.Arg253Ter 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-gln405ter (accessed [today's date]).

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