Is CSNK1D p.Asp385= (c.1155C>T) pathogenic?

CSNK1D p.Asp385= (c.1155C>T) is classified Likely benign in CSNK1D (ClinVar, Single submitter, 1 submitter; last evaluated 2022-04-01). Very rare (popmax 0.00134%, afr).

How common is CSNK1D p.Asp385= (c.1155C>T) in the general population?

CSNK1D p.Asp385= (c.1155C>T) is very rare (popmax 0.00134%, afr) (gnomAD).

CSNK1D p.Asp385=

c.1155C>T · rs1435700605 · VCV2648493

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

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 -0.034	GERP -3.7, phastCons 0.063
Overall
CADD	7.645	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00134% African / African-American · 1/74,862 alleles

Filtering AF 0.000543% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000429%

Overall 0.000808% 13/1,609,228 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00134%	74,862
European (non-Finnish)	0.00102%	98,131

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: CSNK1D
Protein: p.Asp385=
Coding: c.1155C>T
MANE Select: NM_001893
dbSNP: rs1435700605
Type: single nucleotide variant
Location: chr17:82248917 (GRCh38)
Gene constraint: LOEUF 0.512 · pLI 0.97 (gnomAD)
Structure: AlphaFold pLDDT 82.10 · 53 PDB
Residue 385: the 'disordered' region

Full CSNK1D gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CSNK1D p.Ala304= Benign ★★ same type
CSNK1D p.Cys71= Benign/Likely benign ★★ same type
CSNK1D p.Ala30Val Uncertain significance ★ ⚠ same type
CSNK1D p.Ala36Thr Uncertain significance ★ same type
CSNK1D p.Arg306Trp Uncertain significance ★ ⚠ same type
CSNK1D p.Arg311Gln Uncertain significance ★ ⚠ same type
CSNK1D p.Arg314Gln Uncertain significance ★ ⚠ same type
CSNK1D p.Arg324Cys 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/csnk1d-p-asp385 (accessed [today's date]).

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