Is CDIN1 p.Gln139= (c.417G>A) pathogenic?

CDIN1 p.Gln139= (c.417G>A) is classified Likely benign in CDIN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-26). Very rare (popmax 0.000857%, nfe).

How common is CDIN1 p.Gln139= (c.417G>A) in the general population?

CDIN1 p.Gln139= (c.417G>A) is very rare (popmax 0.000857%, nfe) (gnomAD).

CDIN1 p.Gln139=

c.417G>A · VCV4696513

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000857%, nfe)

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 5.9	GERP 2.2, phastCons 1
Overall
CADD	8.782	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000857% European (non-Finnish) · 10/1,166,550 alleles

Filtering AF 0.000434% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000316%

Overall 0.00107% 17/1,593,330 alleles · very rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.00971%	10,299
Finnishnot grpmax-eligible	0.00158%	63,278
European (non-Finnish)grpmax	0.000857%	116,655

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: CDIN1
Protein: p.Gln139=
Coding: c.417G>A
MANE Select: NM_001321759
Type: single nucleotide variant
Location: chr15:36691755 (GRCh38)
Gene constraint: LOEUF 0.931 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 93.59

Full CDIN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDIN1 p.Gln139Glu Uncertain significance ★ ⚠ same residue
CDIN1 p.Ala100Ser Uncertain significance ★★ ⚠ same type
CDIN1 p.Arg101Trp Uncertain significance ★★ ⚠ same type
CDIN1 p.Glu66Ala Uncertain significance ★★ ⚠ same type
CDIN1 p.Pro33Leu Uncertain significance ★★ ⚠ same type
CDIN1 p.Thr271Lys Uncertain significance ★★ ⚠ same type
CDIN1 p.Tyr236Cys Uncertain significance ★★ ⚠ same type
CDIN1 p.Val203Phe 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/cdin1-p-gln139 (accessed [today's date]).

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