Is CKM p.Ter382Gln (c.1144T>C) pathogenic?

CKM p.Ter382Gln (c.1144T>C) is classified Likely benign in CKM (ClinVar, Single submitter, 1 submitter; last evaluated 2019-12-31). Rare (popmax 0.106%, nfe).

How common is CKM p.Ter382Gln (c.1144T>C) in the general population?

CKM p.Ter382Gln (c.1144T>C) is rare (popmax 0.106%, nfe) (gnomAD).

CKM p.Ter382Gln

c.1144T>C · rs142092440 · VCV784717

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

stop-loss

predicted LoF

gnomAD v4.1

Rare

rare (popmax 0.106%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	stop-loss	predicted loss-of-function
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.4, phastCons 1
Overall
CADD	16.49	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

Grpmax group 0.106% European (non-Finnish) · 1,250/1,180,002 alleles

Filtering AF 0.101% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0991%

Overall 0.103% 1,667/1,614,078 alleles · rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.416%	240
European (non-Finnish)grpmax	0.106%	944
Remaining individualsnot grpmax-eligible	0.0912%	1,097
Ashkenazi Jewishnot grpmax-eligible	0.0878%	1,139
Admixed American	0.0866%	1,154
African / African-American	0.0147%	6,821
East Asian	0.00891%	11,220
South Asian	0.0011%	91,080

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: CKM
Protein: p.Ter382Gln
Coding: c.1144T>C
MANE Select: NM_001824
dbSNP: rs142092440
Type: single nucleotide variant
Location: chr19:45306752 (GRCh38)
Gene constraint: LOEUF 1.088 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.92 · 2 PDB

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

Similar variants

CKM p.Leu127Val Uncertain significance ★★ ⚠ same type
CKM p.Pro91Ser Uncertain significance ★★ ⚠ same type
CKM p.Arg251Pro Likely benign ★★ ⚠ same type
CKM p.Ala214Thr Uncertain significance ★ ⚠ same type
CKM p.Ala267Asp Uncertain significance ★ ⚠ same type
CKM p.Ala267Val Uncertain significance ★ ⚠ same type
CKM p.Arg135Gly Uncertain significance ★ ⚠ same type
CKM p.Arg135His 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/ckm-p-ter382gln (accessed [today's date]).

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