Is CDPF1 p.Met37Arg (c.110T>G) pathogenic?

CDPF1 p.Met37Arg (c.110T>G) is classified Uncertain significance in CDPF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-23). AlphaMissense: ambiguous (0.3681); Absent from gnomAD v4.1.

How common is CDPF1 p.Met37Arg (c.110T>G) in the general population?

CDPF1 p.Met37Arg (c.110T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDPF1 p.Met37Arg (c.110T>G)?

AlphaMissense predicts ambiguous (score 0.3681) — an in-silico prediction, not a clinical call.

CDPF1 p.Met37Arg

c.110T>G · rs2518715387 · VCV2477325

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3681 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.3681	ambiguous
REVEL	0.165	moderately benign-leaning
SaProt	LLR -8.75	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	Δ0.22	donor loss · deltas
Pangolin	Δ0.36	loss · gain 0.05 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 11	GERP 1.7, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 3,189 bp · p 0.73 · regional, not allelic
Overall
CADD	21.6	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: CDPF1
Protein: p.Met37Arg
Coding: c.110T>G
MANE Select: NM_207327
dbSNP: rs2518715387
Type: single nucleotide variant
Location: chr22:46248175 (GRCh38)
Gene constraint: LOEUF 1.566 · pLI 0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.30

Full CDPF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDPF1 p.Arg102Trp Uncertain significance ★ ⚠ same type
CDPF1 p.Arg8Cys Uncertain significance ★ ⚠ same type
CDPF1 p.Arg8His Uncertain significance ★ ⚠ same type
CDPF1 p.Arg91Trp Uncertain significance ★ ⚠ same type
CDPF1 p.Cys64Arg Uncertain significance ★ ⚠ same type
CDPF1 p.Cys86Phe Uncertain significance ★ ⚠ same type
CDPF1 p.Glu41Lys Uncertain significance ★ ⚠ same type
CDPF1 p.Glu92Lys 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/cdpf1-p-met37arg (accessed [today's date]).

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