Is DCHS1 p.Arg1788= (c.5364C>T) pathogenic?

DCHS1 p.Arg1788= (c.5364C>T) is classified Likely benign in DCHS1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-04). Absent from gnomAD v4.1.

How common is DCHS1 p.Arg1788= (c.5364C>T) in the general population?

DCHS1 p.Arg1788= (c.5364C>T) is absent from gnomAD v4.1 (gnomAD).

DCHS1 p.Arg1788=

c.5364C>T · VCV3689651

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -0.66	GERP -3
Overall
CADD	5.52	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DCHS1
Protein: p.Arg1788=
Coding: c.5364C>T
MANE Select: NM_003737
Type: single nucleotide variant
Location: chr11:6628628 (GRCh38)
Gene constraint: LOEUF 0.491 · pLI 0.33 · ClinGen HI 1/3 (gnomAD)
Residue 1788: the cadherin 17 domain

Full DCHS1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DCHS1 p.Arg1788Cys Uncertain significance ★★ ⚠ same residue
DCHS1 p.Arg1788His Conflicting classifications of pathogenicity ★ ⚠ same residue
DCHS1 p.Arg1788Leu Uncertain significance ★ ⚠ same residue
DCHS1 p.Arg2141Ter Pathogenic/Likely pathogenic ★★ same type
DCHS1 p.Arg2330Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
DCHS1 p.Ala1241Val Uncertain significance ★★ same type
DCHS1 p.Ala1325Ser Uncertain significance ★★ ⚠ same type
DCHS1 p.Ala142Thr 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/dchs1-p-arg1788 (accessed [today's date]).

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