Is CDIN1 p.Lys50= (c.150A>G) pathogenic?

CDIN1 p.Lys50= (c.150A>G) is classified Uncertain significance in CDIN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-18). Very rare (popmax 0.00244%, eas).

How common is CDIN1 p.Lys50= (c.150A>G) in the general population?

CDIN1 p.Lys50= (c.150A>G) is very rare (popmax 0.00244%, eas) (gnomAD).

CDIN1 p.Lys50=

c.150A>G · rs2040264341 · VCV1949053

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00244%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.46	acceptor gain · deltas
Pangolin	Δ0.22	gain · loss 0.01 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 2.6	GERP -2, phastCons 1
Overall
CADD	7.576	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00244% East Asian · 1/41,000 alleles

Overall 0.000286% 4/1,399,238 alleles · very rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.00499%	20,037
East Asiangrpmax	0.00244%	41,000

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.Lys50=
Coding: c.150A>G
MANE Select: NM_001321759
dbSNP: rs2040264341
Type: single nucleotide variant
Location: chr15:36645225 (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.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
CDIN1 c.148-19G>T Benign/Likely benign ★★ 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-lys50 (accessed [today's date]).

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