Is CHM p.Asp183fs (c.549_557delinsAGTTTTCT) pathogenic?

CHM p.Asp183fs (c.549557delinsAGTTTTCT) is classified Pathogenic in CHM (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-06).

CHM p.Asp183fs

c.549_557delinsAGTTTTCT · VCV3639168

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 5 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.5	GERP 0.78, phastCons 0.68

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

Variant & gene context

Gene: CHM
Protein: p.Asp183fs
Coding: c.549_557delinsAGTTTTCT
MANE Select: NM_000390
Type: Indel
Location: chrX:85963810 (GRCh38)
Structure: AlphaFold pLDDT 81.05

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

Similar variants

CHM c.117-546_126delinsAA Pathogenic ★ same type
CHM c.1465_1510+677delinsTACAAAAGTATTACCTCTTAATACCTCAAGTAGACCCACAATGCAAAAGTTATTAAGAGGTAGGGGCTTTGGAAGATGGTTAGATAACAAGAGCTCTGCCCTCATAAATGGGATTAGTGCTCTTAAAAAAGGGTTCAAGGAAGCTTTTTTATCCCCTTGCCTGTATGAGGACACACAGAAGGTGCCACTTATGAGGAAAGGGTCCTCATCAGACACTGAATCTGCTGGCACCTTGATTTTGGACTTTCCAGCCTCTAGAATTGTGAGCAATAAATTTCTATTGTTTATTATAAGTTACCCAGTCTAAGGTATTTTTTCATAGCAGCCCAAATGGACTAAGAAAGTAAAGAAAAAAAATTAACAATAAAAAAAATGTTATGCAACCAGGTTTTCAATAAGCTAAATAAAAATTAGAATTGAAAGTCATAAAATTCCTTAACTGGAGAACTAAAACATCATGCTTGTGAAGATTTAGCCACTGAAATGTTTATAGGTAAGGGGATGGTGTGAAATGACTTACTCTATAACCATCTTTTATATAAACAAAAACTGTGAATAATAAAAAAGTAAGAAAATCTCTACAAATACAACCTTCACAACTGTAATAACTGCCCCCTTTACCCCCTAAACAAACACAAAATACAAATAACCACTCTACTATGCTTACAGGTGCCTTTCATGCATGTCATCGTTGAAG Pathogenic ★ same type
CHM c.1510+2_1510+19delinsGTTATTTG Likely pathogenic ★ same type
CHM c.703-1_727delinsTTAGAT Pathogenic ★ same type
CHM p.Cys388fs Pathogenic ★ same type
CHM p.Ile14fs Pathogenic ★ same type
CHM p.Ser453fs Pathogenic ★ same type
CHM p.Cys386Ala 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/chm-p-asp183fs (accessed [today's date]).

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