Is CDAN1 p.Arg10= (c.28C>A) pathogenic?

CDAN1 p.Arg10= (c.28C>A) is classified Likely benign in CDAN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-25). Ultra-rare (popmax 0.0378%, afr).

How common is CDAN1 p.Arg10= (c.28C>A) in the general population?

CDAN1 p.Arg10= (c.28C>A) is ultra-rare (popmax 0.0378%, afr) (gnomAD).

CDAN1 p.Arg10=

c.28C>A · rs543368542 · VCV2961244

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0378%, 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 4.5	GERP -0.59, phastCons 1
Overall
CADD	12.82	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0378% African / African-American · 27/71,400 alleles

Filtering AF 0.0266% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0229%

Overall 0.00367% 56/1,526,512 alleles · ultra-rare exomes 43/1,374,548 · genomes 13/151,964 · joint denominator

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0479%	2,089
African / African-Americangrpmax	0.0378%	2,644
Admixed American	0.00201%	49,738

Remaining individuals 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: CDAN1
Protein: p.Arg10=
Coding: c.28C>A
MANE Select: NM_138477
dbSNP: rs543368542
Type: single nucleotide variant
Location: chr15:42737075 (GRCh38)
Gene constraint: LOEUF 0.908 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 72.58 · 2 PDB

Full CDAN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDAN1 p.Arg1042Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
CDAN1 p.Arg682Ter Pathogenic ★★ same type
CDAN1 p.Arg714Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
CDAN1 p.Asn599Ser Likely pathogenic ★★ ⚠ same type
CDAN1 p.Phe52Leu Pathogenic/Likely pathogenic ★★ ⚠ same type
CDAN1 p.Pro1130Leu Pathogenic/Likely pathogenic ★★ same type
CDAN1 p.Pro51Leu Likely pathogenic ★★ ⚠ same type
CDAN1 p.Pro672Leu Pathogenic/Likely pathogenic ★★ ⚠ 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/cdan1-p-arg10 (accessed [today's date]).

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